Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades.py --pe1-1 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end1.fastq.gz --pe1-2 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end2.fastq.gz --pe2-1 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end1_val_1.fq.gz --pe2-2 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end2_val_2.fq.gz -o /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only System information: SPAdes version: 3.15.4 Python version: 3.10.9 OS: Linux-4.15.0-213-generic-x86_64-with-glibc2.27 Output dir: /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Standard mode For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end1.fastq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end2.fastq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Library number: 2, library type: paired-end orientation: fr left reads: ['/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end1_val_1.fq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end2_val_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/tmp Threads: 16 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/spades.log /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end1.fastq.gz: max reads length: 38 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end2.fastq.gz: max reads length: 38 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end1_val_1.fq.gz: max reads length: 149 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end2_val_2.fq.gz: max reads length: 149 Reads length: 149 ===== Before start started. ===== Read error correction started. ===== Read error correction started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades-hammer /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/configs/config.info 0:00:00.000 1M / 33M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.15.4, git revision 1a5332e5608a073a9d28a6d0e30836f38dcc5613 0:00:00.009 1M / 33M INFO General (main.cpp : 76) Loading config from /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/configs/config.info 0:00:00.012 1M / 33M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.012 1M / 33M INFO General (memory_limit.cpp : 54) Memory limit set to 250 Gb 0:00:00.012 1M / 33M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.014 1M / 33M INFO General (main.cpp : 92) Determined value is 33 0:00:00.015 1M / 33M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.015 1M / 33M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.018 1M / 33M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 16 files using 16 threads. This might take a while. 0:00:00.021 1M / 33M INFO General (file_limit.hpp : 42) Open file limit set to 1024 0:00:00.022 1M / 33M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.20833 Gb 0:00:00.022 1M / 33M INFO General (kmer_splitter.hpp : 101) Using cell size of 4194304 0:00:00.023 9217M / 9217M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end1.fastq.gz 0:00:23.773 9217M / 9217M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 6930328 reads 0:00:23.774 9217M / 9217M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end2.fastq.gz 0:00:46.677 9217M / 9217M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 13860656 reads 0:00:46.678 9217M / 9217M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end1_val_1.fq.gz 0:01:20.354 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 21517462 reads 0:01:54.342 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 29176994 reads 0:02:28.577 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 36843053 reads 0:03:00.417 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 44351398 reads 0:03:30.349 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 52204293 reads 0:03:59.011 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 59670674 reads 0:04:27.584 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 67317680 reads 0:04:56.435 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 74939587 reads 0:05:24.394 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 82279728 reads 0:05:54.137 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 89919170 reads 0:06:11.477 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end2_val_2.fq.gz 0:09:03.799 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 138414771 reads 0:11:23.331 9217M / 15G INFO K-mer Splitting (kmer_data.cpp : 112) Total 174687072 reads processed 0:11:23.332 1M / 15G INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:11:53.213 1M / 15G INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 277829158 kmers in total. 0:11:53.216 1M / 15G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:12:00.287 211M / 15G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 277829158 kmers, 200677736 bytes occupied (5.77845 bits per kmer). 0:12:00.287 211M / 15G INFO K-mer Counting (kmer_data.cpp : 354) Arranging kmers in hash map order 0:12:10.527 4451M / 15G INFO General (main.cpp : 148) Clustering Hamming graph. 0:16:13.955 4451M / 15G INFO General (main.cpp : 155) Extracting clusters: 0:16:13.955 4451M / 15G INFO General (concurrent_dsu.cpp : 18) Connecting to root 0:16:14.829 4451M / 15G INFO General (concurrent_dsu.cpp : 34) Calculating counts 0:17:00.654 6627M / 15G INFO General (concurrent_dsu.cpp : 63) Writing down entries 0:19:00.061 4451M / 15G INFO General (main.cpp : 167) Clustering done. Total clusters: 76061476 0:19:00.176 2331M / 15G INFO K-mer Counting (kmer_data.cpp : 371) Collecting K-mer information, this takes a while. 0:19:03.469 8691M / 15G INFO K-mer Counting (kmer_data.cpp : 377) Processing /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end1.fastq.gz 0:19:16.932 8691M / 15G INFO K-mer Counting (kmer_data.cpp : 377) Processing /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end2.fastq.gz 0:19:30.346 8691M / 15G INFO K-mer Counting (kmer_data.cpp : 377) Processing /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end1_val_1.fq.gz 0:26:25.106 8691M / 15G INFO K-mer Counting (kmer_data.cpp : 377) Processing /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end2_val_2.fq.gz 0:33:23.540 8691M / 15G INFO K-mer Counting (kmer_data.cpp : 384) Collection done, postprocessing. 0:33:24.490 8691M / 15G INFO K-mer Counting (kmer_data.cpp : 397) There are 277829158 kmers in total. Among them 207445320 (74.6665%) are singletons. 0:33:24.490 8691M / 15G INFO General (main.cpp : 173) Subclustering Hamming graph 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering done. Total 3283 non-read kmers were generated. 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Subclustering statistics: 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton hamming clusters: 53153240. Among them 4045030 (7.61013%) are good 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total singleton subclusters: 109732. Among them 107752 (98.1956%) are good 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Total non-singleton subcluster centers: 25215594. Among them 22319535 (88.5148%) are good 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average size of non-trivial subcluster: 8.91066 kmers 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Average number of sub-clusters per non-singleton cluster: 1.10551 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Total solid k-mers: 26472317 0:36:17.823 8691M / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 658) Substitution probabilities: [4,4]((0.928432,0.0465453,0.0165232,0.00849929),(0.0202958,0.955368,0.00572839,0.0186081),(0.0178439,0.00569209,0.955747,0.0207171),(0.00832293,0.016991,0.0464394,0.928247)) 0:36:17.889 8691M / 15G INFO General (main.cpp : 178) Finished clustering. 0:36:17.889 8691M / 15G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. 0:41:35.000 8691M / 15G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 4012078 new k-mers. 0:46:52.026 8691M / 15G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 491402 new k-mers. 0:52:08.228 8691M / 15G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 40960 new k-mers. 0:57:25.561 8691M / 15G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 5340 new k-mers. 1:02:42.339 8691M / 15G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 1218 new k-mers. 1:07:59.524 8691M / 15G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 182 new k-mers. 1:13:30.460 8691M / 15G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 19 new k-mers. 1:19:17.720 8691M / 15G INFO General (main.cpp : 218) Solid k-mers iteration 7 produced 0 new k-mers. 1:19:17.720 8691M / 15G INFO General (main.cpp : 222) Solid k-mers finalized 1:19:17.720 8691M / 15G INFO General (hammer_tools.cpp : 222) Starting read correction in 16 threads. 1:19:17.720 8691M / 15G INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end1.fastq.gz and /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789+L2790-yeast_YAC_Matt_1.36mers.end2.fastq.gz 1:19:21.977 9504M / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 0 of 1600000 reads. 1:19:25.183 9689M / 15G INFO General (hammer_tools.cpp : 177) Processed batch 0 1:19:26.703 9689M / 15G INFO General (hammer_tools.cpp : 187) Written batch 0 1:19:29.916 9692M / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 1 of 1600000 reads. 1:19:32.271 9699M / 15G INFO General (hammer_tools.cpp : 177) Processed batch 1 1:19:33.765 9699M / 15G INFO General (hammer_tools.cpp : 187) Written batch 1 1:19:36.769 9699M / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 2 of 1600000 reads. 1:19:39.819 9699M / 15G INFO General (hammer_tools.cpp : 177) Processed batch 2 1:19:41.375 9699M / 15G INFO General (hammer_tools.cpp : 187) Written batch 2 1:19:44.705 9699M / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 3 of 1600000 reads. 1:19:46.916 9699M / 15G INFO General (hammer_tools.cpp : 177) Processed batch 3 1:19:48.377 9699M / 15G INFO General (hammer_tools.cpp : 187) Written batch 3 1:19:49.373 9699M / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 4 of 530328 reads. 1:19:50.146 9699M / 15G INFO General (hammer_tools.cpp : 177) Processed batch 4 1:19:50.625 9699M / 15G INFO General (hammer_tools.cpp : 187) Written batch 4 1:20:25.615 8691M / 15G INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end1_val_1.fq.gz and /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end2_val_2.fq.gz 1:20:30.302 10G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 0 of 1600000 reads. 1:20:36.848 10G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 0 1:20:39.131 10G / 15G INFO General (hammer_tools.cpp : 187) Written batch 0 1:20:44.070 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 1 of 1600000 reads. 1:20:51.365 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 1 1:20:53.895 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 1 1:20:59.159 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 2 of 1600000 reads. 1:21:06.437 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 2 1:21:56.427 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 2 1:22:01.209 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 3 of 1600000 reads. 1:22:08.032 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 3 1:22:11.156 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 3 1:22:16.018 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 4 of 1600000 reads. 1:22:23.072 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 4 1:22:26.061 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 4 1:22:30.822 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 5 of 1600000 reads. 1:22:37.636 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 5 1:23:21.046 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 5 1:23:25.835 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 6 of 1600000 reads. 1:23:32.228 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 6 1:23:34.973 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 6 1:23:39.697 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 7 of 1600000 reads. 1:23:46.256 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 7 1:24:12.401 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 7 1:24:17.398 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 8 of 1600000 reads. 1:24:24.714 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 8 1:24:36.894 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 8 1:24:41.443 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 9 of 1600000 reads. 1:24:47.802 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 9 1:24:50.636 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 9 1:24:55.219 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 10 of 1600000 reads. 1:25:01.440 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 10 1:25:31.086 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 10 1:25:36.174 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 11 of 1600000 reads. 1:25:43.404 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 11 1:25:46.552 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 11 1:25:51.576 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 12 of 1600000 reads. 1:25:58.856 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 12 1:26:31.924 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 12 1:26:36.478 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 13 of 1600000 reads. 1:26:42.668 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 13 1:26:58.618 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 13 1:27:03.232 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 14 of 1600000 reads. 1:27:09.836 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 14 1:27:12.646 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 14 1:27:17.380 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 15 of 1600000 reads. 1:27:24.024 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 15 1:27:50.938 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 15 1:27:55.689 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 16 of 1600000 reads. 1:28:02.231 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 16 1:28:20.516 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 16 1:28:25.073 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 17 of 1600000 reads. 1:28:31.539 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 17 1:28:54.552 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 17 1:28:59.204 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 18 of 1600000 reads. 1:29:06.028 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 18 1:29:13.654 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 18 1:29:18.290 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 19 of 1600000 reads. 1:29:25.064 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 19 1:29:28.260 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 19 1:29:33.138 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 20 of 1600000 reads. 1:29:39.254 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 20 1:29:53.841 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 20 1:29:58.695 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 21 of 1600000 reads. 1:30:05.623 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 21 1:30:16.892 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 21 1:30:22.046 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 22 of 1600000 reads. 1:30:28.357 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 22 1:30:31.359 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 22 1:30:36.341 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 23 of 1600000 reads. 1:30:42.782 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 23 1:30:56.692 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 23 1:31:01.423 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 24 of 1600000 reads. 1:31:08.261 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 24 1:31:19.292 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 24 1:31:24.221 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 25 of 1600000 reads. 1:31:30.836 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 25 1:31:33.859 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 25 1:31:38.554 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 26 of 1600000 reads. 1:31:45.598 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 26 1:31:58.786 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 26 1:32:03.821 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 27 of 1600000 reads. 1:32:11.342 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 27 1:32:31.655 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 27 1:32:36.716 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 28 of 1600000 reads. 1:32:43.857 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 28 1:32:52.638 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 28 1:32:57.228 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 29 of 1600000 reads. 1:33:04.634 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 29 1:33:07.532 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 29 1:33:12.467 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 30 of 1600000 reads. 1:33:19.990 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 30 1:33:39.146 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 30 1:33:44.123 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 31 of 1600000 reads. 1:33:51.425 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 31 1:33:54.751 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 31 1:33:59.259 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 32 of 1600000 reads. 1:34:06.194 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 32 1:34:09.164 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 32 1:34:13.994 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 33 of 1600000 reads. 1:34:21.222 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 33 1:34:34.585 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 33 1:34:39.748 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 34 of 1600000 reads. 1:34:47.161 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 34 1:35:01.739 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 34 1:35:06.760 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 35 of 1600000 reads. 1:35:14.153 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 35 1:35:33.296 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 35 1:35:38.298 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 36 of 1600000 reads. 1:35:45.518 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 36 1:35:55.603 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 36 1:36:00.411 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 37 of 1600000 reads. 1:36:07.680 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 37 1:36:10.687 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 37 1:36:15.727 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 38 of 1600000 reads. 1:36:22.819 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 38 1:36:38.503 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 38 1:36:43.628 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 39 of 1600000 reads. 1:36:50.864 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 39 1:36:53.787 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 39 1:36:58.679 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 40 of 1600000 reads. 1:37:06.058 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 40 1:37:12.658 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 40 1:37:17.535 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 41 of 1600000 reads. 1:37:25.013 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 41 1:37:43.015 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 41 1:37:47.618 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 42 of 1600000 reads. 1:37:54.710 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 42 1:38:10.068 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 42 1:38:14.709 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 43 of 1600000 reads. 1:38:21.828 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 43 1:38:24.790 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 43 1:38:29.529 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 44 of 1600000 reads. 1:38:37.071 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 44 1:38:39.943 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 44 1:38:44.554 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 45 of 1600000 reads. 1:38:51.850 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 45 1:38:54.642 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 45 1:38:59.179 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 46 of 1600000 reads. 1:39:06.170 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 46 1:39:21.804 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 46 1:39:26.583 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 47 of 1600000 reads. 1:39:33.573 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 47 1:39:37.280 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 47 1:39:42.084 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 48 of 1600000 reads. 1:39:49.036 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 48 1:39:52.007 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 48 1:39:56.795 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 49 of 1600000 reads. 1:40:03.270 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 49 1:40:19.473 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 49 1:40:20.653 11G / 15G INFO General (hammer_tools.cpp : 170) Prepared batch 50 of 413208 reads. 1:40:22.431 11G / 15G INFO General (hammer_tools.cpp : 177) Processed batch 50 1:44:21.748 11G / 15G INFO General (hammer_tools.cpp : 187) Written batch 50 1:44:25.186 8691M / 15G INFO General (hammer_tools.cpp : 276) Correction done. Changed 13242582 bases in 9132371 reads. 1:44:25.271 8691M / 15G INFO General (hammer_tools.cpp : 277) Failed to correct 499875 bases out of 13929382079. 1:44:25.840 1M / 15G INFO General (main.cpp : 255) Saving corrected dataset description to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/corrected.yaml 1:44:25.970 1M / 15G INFO General (main.cpp : 262) All done. Exiting. ===== Read error correction finished. ===== corrected reads compression started. == Running: /users/marinovg/miniconda3/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/scripts/compress_all.py --input_file /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/corrected.yaml --ext_python_modules_home /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades --max_threads 16 --output_dir /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected --gzip_output == Compressing corrected reads (with pigz) == Files to compress: ['/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/L2789+L2790-yeast_YAC_Matt_1.36mers.end1.fastq.00.0_0.cor.fastq', '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/L2789+L2790-yeast_YAC_Matt_1.36mers.end2.fastq.00.0_0.cor.fastq', '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/L2789+L2790-yeast_YAC_Matt_1.36mers.end_unpaired.00.0_0.cor.fastq', '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end1_val_1.fq.00.1_0.cor.fastq', '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end2_val_2.fq.00.1_0.cor.fastq', '/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/L2789-yeast_YAC_Matt_1.CKDL230018740-1A_225KKJLT3_L2.end_unpaired.00.1_0.cor.fastq'] == Files compression is finished == Dataset yaml file is updated ===== corrected reads compression finished. ===== Read error correction finished. ===== Assembling started. ===== K21 started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades-core /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K21/configs/config.info 0:00:00.000 1M / 33M INFO General (main.cpp : 99) Loaded config from /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K21/configs/config.info 0:00:00.001 1M / 33M INFO General (memory_limit.cpp : 54) Memory limit set to 250 Gb 0:00:00.001 1M / 33M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.4, git revision 1a5332e5608a073a9d28a6d0e30836f38dcc5613 0:00:00.001 1M / 33M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.001 1M / 33M INFO General (main.cpp : 109) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/dataset.info) with K=21 0:00:00.001 1M / 33M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.001 1M / 33M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.001 1M / 33M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.001 1M / 33M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:00:00.001 1M / 33M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.081 1M / 33M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.081 1M / 33M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.447 21M / 36M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:00.454 21M / 38M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:00.462 21M / 40M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:00.577 18M / 56M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:00.742 15M / 68M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:01.141 9M / 92M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:01.955 0M / 115M INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:03.624 0M / 152M INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:06.627 0M / 164M INFO General (binary_converter.cpp : 96) 4194304 reads processed 0:00:09.911 0M / 166M INFO General (binary_converter.cpp : 111) 6435597 reads written 0:00:09.911 0M / 166M INFO General (read_converter.cpp : 86) Converting single reads 0:00:10.031 0M / 166M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:10.035 0M / 166M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:10.042 0M / 166M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:10.183 0M / 166M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:10.357 0M / 166M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:10.560 0M / 167M INFO General (binary_converter.cpp : 111) 437926 reads written 0:00:10.560 0M / 167M INFO General (read_converter.cpp : 92) Converting merged reads 0:00:10.564 0M / 167M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:14.528 0M / 167M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #1 (takes a while) 0:00:14.528 0M / 167M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:15.247 0M / 167M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:15.255 0M / 167M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:15.266 0M / 167M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:15.497 0M / 174M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:15.714 0M / 174M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:16.161 0M / 181M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:17.124 0M / 197M INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:19.046 0M / 236M INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:23.118 0M / 261M INFO General (binary_converter.cpp : 96) 4194304 reads processed 0:00:31.407 0M / 295M INFO General (binary_converter.cpp : 96) 8388608 reads processed 0:00:58.353 0M / 295M INFO General (binary_converter.cpp : 96) 16777216 reads processed 0:01:38.263 0M / 315M INFO General (binary_converter.cpp : 96) 33554432 reads processed 0:03:06.788 0M / 315M INFO General (binary_converter.cpp : 96) 67108864 reads processed 0:03:39.146 0M / 339M INFO General (binary_converter.cpp : 111) 79693563 reads written 0:03:39.146 0M / 339M INFO General (read_converter.cpp : 86) Converting single reads 0:03:40.668 0M / 339M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:03:40.673 0M / 339M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:03:40.682 0M / 339M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:03:40.860 0M / 339M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:03:41.135 0M / 339M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:03:41.505 0M / 339M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:03:41.579 0M / 339M INFO General (binary_converter.cpp : 111) 547515 reads written 0:03:41.579 0M / 339M INFO General (read_converter.cpp : 92) Converting merged reads 0:03:41.583 0M / 339M INFO General (binary_converter.cpp : 111) 0 reads written 0:03:45.423 1M / 339M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:03:45.513 2M / 339M INFO General (construction.cpp : 153) Max read length 149 0:03:45.513 2M / 339M INFO General (construction.cpp : 159) Average read length 80.1405 0:03:45.513 2M / 339M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:03:45.513 2M / 339M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 160 files using 16 threads. This might take a while. 0:03:45.518 2M / 339M INFO General (file_limit.hpp : 42) Open file limit set to 1024 0:03:45.518 2M / 339M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.20831 Gb 0:03:45.518 2M / 339M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:04:21.222 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 49305802 reads 0:04:50.232 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 78283913 reads 0:05:17.534 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 107066054 reads 0:05:46.144 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 135965096 reads 0:06:14.429 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 164855304 reads 0:06:44.074 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 193685411 reads 0:07:10.532 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 222582352 reads 0:07:38.308 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 251415498 reads 0:08:04.758 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 280320093 reads 0:08:38.432 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 309399985 reads 0:09:11.555 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 338183569 reads 0:09:38.115 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 346487522 reads 0:09:38.139 2M / 9147M INFO General (kmer_splitters.hpp : 131) Used 346487522 reads 0:09:38.584 2M / 9147M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:09:42.217 2M / 9147M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 33177041 kmers in total. 0:09:42.218 2M / 9147M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:09:42.497 2M / 9147M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:09:42.497 2M / 9147M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 160 files using 16 threads. This might take a while. 0:09:42.501 2M / 9147M INFO General (file_limit.hpp : 42) Open file limit set to 1024 0:09:42.501 2M / 9147M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.20831 Gb 0:09:42.501 2M / 9147M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:10:12.085 9602M / 9602M INFO General (kmer_splitters.hpp : 194) Processed 33177041 kmers 0:10:12.088 9602M / 9602M INFO General (kmer_splitters.hpp : 199) Used 33177041 kmers. 0:10:12.095 2M / 9147M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:10:15.773 2M / 9147M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 32114288 kmers in total. 0:10:15.775 2M / 9147M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:10:16.248 27M / 9147M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 32114288 kmers, 23313688 bytes occupied (5.80768 bits per kmer). 0:10:16.248 27M / 9147M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:10:19.760 58M / 9147M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:10:21.010 58M / 9147M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:10:21.163 58M / 9147M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 0:10:21.163 58M / 9147M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 0:10:21.163 58M / 9147M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 0:10:22.446 137M / 9147M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 1248167 0:10:22.502 137M / 9147M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 1294209 0:10:22.513 58M / 9147M INFO Early tip clipping (early_simplification.hpp : 49) 7608463 22-mers were removed by early tip clipper 0:10:22.513 58M / 9147M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:10:22.702 58M / 9147M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:10:23.940 153M / 9147M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2744281 sequences extracted 0:10:24.664 153M / 9147M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:10:25.039 153M / 9147M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 17 loops collected 0:10:25.194 153M / 9147M INFO General (debruijn_graph_constructor: 487) Total 5488596 edges to create 0:10:25.194 366M / 9147M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:10:27.762 450M / 9147M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:10:27.821 450M / 9147M INFO General (debruijn_graph_constructor: 493) Sorting done 0:10:27.854 466M / 9147M INFO General (debruijn_graph_constructor: 503) Total 1681545 vertices to create 0:10:27.855 623M / 9147M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:10:29.655 480M / 9147M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:10:29.655 480M / 9147M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:10:30.018 505M / 9147M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 33177041 kmers, 24081256 bytes occupied (5.80673 bits per kmer). 0:10:30.094 634M / 9147M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:12:38.259 634M / 9147M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:12:39.316 634M / 9147M INFO General (coverage_filling.hpp : 82) Processed 5488495 edges 0:12:39.814 547M / 9147M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:12:40.703 671M / 9147M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 48 0:12:40.726 547M / 9147M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 231 0:12:40.726 547M / 9147M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 233. Coverage mad: 130.469 0:12:40.750 547M / 9147M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:12:41.100 671M / 9147M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:12:41.821 671M / 9147M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:12:44.272 671M / 9147M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:12:48.551 671M / 9147M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:12:53.557 671M / 9147M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:12:57.088 671M / 9147M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 499.178. Fitted coverage std. dev: 369.58 0:12:57.088 671M / 9147M WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 5 0:12:57.092 671M / 9147M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:12:57.092 671M / 9147M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 68 0:12:57.092 671M / 9147M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 68 0:12:57.092 671M / 9147M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 11853643 0:12:57.100 547M / 9147M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 499.178 0:12:57.100 547M / 9147M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 68 0:12:57.100 547M / 9147M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:12:57.100 547M / 9147M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:12:57.100 547M / 9147M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 0:12:57.100 547M / 9147M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:12:57.100 547M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 0:12:57.169 547M / 9147M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 0:12:57.169 547M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 0:12:57.423 547M / 9147M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 34704 times 0:12:57.424 547M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 0:13:03.566 606M / 9147M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 789563 times 0:13:03.573 606M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 0:13:03.637 606M / 9147M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 21036 times 0:13:03.637 512M / 9147M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:13:03.637 512M / 9147M INFO General (simplification.cpp : 368) Graph simplification started 0:13:03.637 512M / 9147M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:13:03.638 512M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:13:03.638 512M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:03.713 512M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 8585 times 0:13:03.713 512M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:08.417 515M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 33559 times 0:13:08.420 515M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:09.759 530M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 164830 times 0:13:09.763 530M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:13:09.763 530M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:09.845 525M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 728 times 0:13:09.845 525M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:11.485 518M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 18512 times 0:13:11.487 518M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:11.706 518M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 31848 times 0:13:11.708 518M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:13:11.708 518M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:11.729 515M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 112 times 0:13:11.729 515M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.179 513M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 6074 times 0:13:12.180 513M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.250 512M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 10009 times 0:13:12.251 512M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:13:12.251 512M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.261 512M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 19 times 0:13:12.261 512M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.480 510M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2022 times 0:13:12.480 510M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.510 511M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 4715 times 0:13:12.511 511M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:13:12.511 511M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.514 510M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 4 times 0:13:12.514 510M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.615 510M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 845 times 0:13:12.616 510M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.633 510M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 2807 times 0:13:12.634 510M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:13:12.634 510M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.636 510M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 6 times 0:13:12.636 510M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.692 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 414 times 0:13:12.692 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.707 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1756 times 0:13:12.707 509M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:13:12.707 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.709 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 5 times 0:13:12.709 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.745 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 192 times 0:13:12.745 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.754 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1513 times 0:13:12.755 509M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:13:12.755 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.756 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:13:12.756 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.781 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 196 times 0:13:12.781 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.788 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1042 times 0:13:12.788 509M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:13:12.788 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.788 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:13:12.788 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.805 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 87 times 0:13:12.805 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.811 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 872 times 0:13:12.811 509M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:13:12.811 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.811 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 5 times 0:13:12.811 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.825 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 68 times 0:13:12.825 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.830 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 709 times 0:13:12.830 509M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:13:12.830 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.836 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 17 times 0:13:12.836 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.920 509M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 80 times 0:13:12.920 509M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.926 500M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:13:12.926 500M / 9147M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 12 0:13:12.926 500M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.926 500M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:12.926 500M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:12.926 500M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:13:12.926 500M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:12.926 500M / 9147M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:13:12.934 499M / 9147M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:13:12.934 499M / 9147M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:13:12.935 499M / 9147M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:13:12.935 499M / 9147M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:13:12.935 499M / 9147M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:13:12.935 499M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:12.940 499M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:12.940 499M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:13.018 499M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:13:13.018 499M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:13.023 499M / 9147M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:13.023 499M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:13.100 499M / 9147M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:13:13.100 499M / 9147M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:13:13.113 499M / 9147M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:13:13.119 499M / 9147M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 55 times 0:13:13.125 499M / 9147M INFO General (simplification.cpp : 495) After simplification: 0:13:13.125 499M / 9147M INFO General (simplification.cpp : 496) Average coverage = 811.163 0:13:13.131 499M / 9147M INFO General (simplification.cpp : 497) Total length = 12588566 0:13:13.139 499M / 9147M INFO General (simplification.cpp : 498) Median edge length: 5381 0:13:13.139 499M / 9147M INFO General (simplification.cpp : 499) Edges: 80003 0:13:13.139 499M / 9147M INFO General (simplification.cpp : 500) Vertices: 55782 0:13:13.139 499M / 9147M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:13:13.141 499M / 9147M INFO General (read_converter.cpp : 107) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K21/simplified_contigs 0:13:13.172 501M / 9147M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:13:13.177 501M / 9147M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:13:13.199 501M / 9147M INFO General (binary_converter.cpp : 111) 40019 reads written 0:13:13.552 499M / 9147M INFO General (pipeline.cpp : 287) SPAdes finished 0:13:13.609 1M / 9147M INFO General (main.cpp : 136) Assembling time: 0 hours 13 minutes 13 seconds ===== K21 finished. ===== K33 started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades-core /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K33/configs/config.info 0:00:00.000 1M / 33M INFO General (main.cpp : 99) Loaded config from /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K33/configs/config.info 0:00:00.001 1M / 33M INFO General (memory_limit.cpp : 54) Memory limit set to 250 Gb 0:00:00.001 1M / 33M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.4, git revision 1a5332e5608a073a9d28a6d0e30836f38dcc5613 0:00:00.001 1M / 33M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.001 1M / 33M INFO General (main.cpp : 109) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/dataset.info) with K=33 0:00:00.001 1M / 33M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.001 1M / 33M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.001 1M / 33M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.001 1M / 33M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:00:00.001 1M / 33M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.004 1M / 33M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.006 1M / 33M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.008 1M / 33M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:00.008 1M / 33M INFO General (construction.cpp : 118) Contigs from previous K will be used: /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K21/simplified_contigs 0:00:00.084 2M / 33M INFO General (construction.cpp : 153) Max read length 149 0:00:00.084 2M / 33M INFO General (construction.cpp : 159) Average read length 80.1405 0:00:00.084 2M / 33M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:00.084 2M / 33M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 160 files using 16 threads. This might take a while. 0:00:00.107 2M / 33M INFO General (file_limit.hpp : 42) Open file limit set to 1024 0:00:00.107 2M / 33M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.20831 Gb 0:00:00.107 2M / 33M INFO General (kmer_splitter.hpp : 101) Using cell size of 209715 0:00:34.253 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 41217334 reads 0:01:01.867 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 57722278 reads 0:01:28.238 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 74246966 reads 0:01:57.849 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 90696707 reads 0:02:29.068 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 107078738 reads 0:03:03.618 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 123529780 reads 0:03:29.532 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 139987080 reads 0:03:54.659 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 156508361 reads 0:04:20.972 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 172967901 reads 0:04:46.431 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 189411546 reads 0:05:14.445 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 205942738 reads 0:05:42.265 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 222356801 reads 0:06:09.600 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 238810735 reads 0:07:03.056 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 271701906 reads 0:09:43.811 2M / 8437M INFO General (kmer_splitters.hpp : 131) Used 346567560 reads 0:09:44.290 2M / 8437M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:09:51.716 2M / 8437M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 42065572 kmers in total. 0:09:51.716 2M / 8437M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:09:51.985 2M / 8437M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:09:51.985 2M / 8437M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 160 files using 16 threads. This might take a while. 0:09:51.989 2M / 8437M INFO General (file_limit.hpp : 42) Open file limit set to 1024 0:09:51.989 2M / 8437M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.20831 Gb 0:09:51.989 2M / 8437M INFO General (kmer_splitter.hpp : 101) Using cell size of 209715 0:10:24.865 9602M / 9602M INFO General (kmer_splitters.hpp : 194) Processed 42065572 kmers 0:10:24.865 9602M / 9602M INFO General (kmer_splitters.hpp : 199) Used 42065572 kmers. 0:10:24.869 2M / 8437M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:10:33.082 2M / 8437M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 41460076 kmers in total. 0:10:33.082 2M / 8437M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:10:33.767 32M / 8437M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 41460076 kmers, 30063888 bytes occupied (5.80103 bits per kmer). 0:10:33.767 32M / 8437M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:10:41.418 72M / 8437M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:10:43.290 72M / 8437M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:10:43.485 71M / 8437M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 0:10:43.485 71M / 8437M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 0:10:43.485 71M / 8437M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 0:10:45.516 230M / 8437M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 1385953 0:10:45.620 230M / 8437M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 1434199 0:10:45.650 71M / 8437M INFO Early tip clipping (early_simplification.hpp : 49) 11568520 34-mers were removed by early tip clipper 0:10:45.650 71M / 8437M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:10:45.834 71M / 8437M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:10:47.538 177M / 8437M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2193612 sequences extracted 0:10:48.478 177M / 8437M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:10:48.991 177M / 8437M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 17 loops collected 0:10:49.152 177M / 8437M INFO General (debruijn_graph_constructor: 487) Total 4387258 edges to create 0:10:49.153 350M / 8437M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:10:51.325 418M / 8437M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:10:51.366 418M / 8437M INFO General (debruijn_graph_constructor: 493) Sorting done 0:10:51.393 434M / 8437M INFO General (debruijn_graph_constructor: 503) Total 1588133 vertices to create 0:10:51.393 583M / 8437M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:10:53.050 464M / 8437M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:10:53.050 464M / 8437M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:10:53.444 499M / 8437M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 42065572 kmers, 30502256 bytes occupied (5.8009 bits per kmer). 0:10:53.537 663M / 8437M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:12:48.082 663M / 8437M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:12:49.430 663M / 8437M INFO General (coverage_filling.hpp : 82) Processed 4387224 edges 0:12:49.988 497M / 8437M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:12:50.652 601M / 8437M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 54 0:12:50.671 497M / 8437M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 186 0:12:50.671 497M / 8437M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 186. Coverage mad: 94.8864 0:12:50.692 497M / 8437M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:12:50.989 601M / 8437M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:12:51.592 601M / 8437M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:12:53.786 601M / 8437M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:12:57.950 601M / 8437M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:13:03.437 601M / 8437M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:13:10.364 601M / 8437M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 400.307. Fitted coverage std. dev: 295.636 0:13:10.364 601M / 8437M WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 4 0:13:10.367 601M / 8437M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:13:10.367 601M / 8437M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 96 0:13:10.367 601M / 8437M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 96 0:13:10.368 601M / 8437M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 11158769 0:13:10.374 497M / 8437M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 400.307 0:13:10.375 497M / 8437M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 96 0:13:10.375 497M / 8437M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:13:10.375 497M / 8437M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:13:10.375 497M / 8437M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 0:13:10.375 497M / 8437M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:13:10.375 497M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 0:13:10.445 497M / 8437M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 3 times 0:13:10.445 497M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 0:13:10.807 496M / 8437M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 56705 times 0:13:10.808 496M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 0:13:15.423 510M / 8437M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 500329 times 0:13:15.435 510M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 0:13:15.699 508M / 8437M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 137326 times 0:13:15.700 450M / 8437M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:13:15.700 450M / 8437M INFO General (simplification.cpp : 368) Graph simplification started 0:13:15.700 450M / 8437M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:13:15.700 450M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:13:15.700 450M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:15.814 449M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 16376 times 0:13:15.816 449M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:20.862 452M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 34163 times 0:13:20.865 452M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:22.481 459M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 155913 times 0:13:22.484 459M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:13:22.485 459M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:22.553 455M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2146 times 0:13:22.554 455M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:24.662 446M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 18146 times 0:13:24.665 446M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:24.813 445M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 15970 times 0:13:24.816 445M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:13:24.816 445M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:24.831 444M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 106 times 0:13:24.831 444M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.102 442M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2572 times 0:13:25.103 442M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.148 442M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 4682 times 0:13:25.149 442M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:13:25.149 442M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.154 442M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 32 times 0:13:25.154 442M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.251 441M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 550 times 0:13:25.251 441M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.275 441M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 2297 times 0:13:25.275 441M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:13:25.275 441M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.277 441M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 13 times 0:13:25.277 441M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.333 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 219 times 0:13:25.334 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.348 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1420 times 0:13:25.348 440M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:13:25.348 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.349 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 5 times 0:13:25.349 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.373 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 107 times 0:13:25.373 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.382 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 908 times 0:13:25.383 440M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:13:25.383 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.383 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 5 times 0:13:25.383 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.403 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 72 times 0:13:25.403 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.409 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 665 times 0:13:25.409 440M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:13:25.409 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.410 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 0:13:25.410 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.425 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 55 times 0:13:25.425 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.430 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 483 times 0:13:25.430 440M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:13:25.430 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.430 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:25.430 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.438 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 36 times 0:13:25.438 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.442 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 352 times 0:13:25.442 440M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:13:25.442 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.442 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 4 times 0:13:25.442 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.447 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 27 times 0:13:25.447 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.450 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 282 times 0:13:25.450 440M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:13:25.450 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.455 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 35 times 0:13:25.455 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.479 440M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 31 times 0:13:25.479 440M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.483 431M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:13:25.483 431M / 8437M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 12 0:13:25.483 431M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.483 431M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:25.483 431M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.484 431M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:13:25.484 431M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:13:25.484 431M / 8437M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:13:25.491 430M / 8437M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:13:25.491 430M / 8437M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:13:25.491 430M / 8437M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:13:25.491 430M / 8437M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:13:25.491 430M / 8437M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:13:25.491 430M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.495 430M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:25.495 430M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.519 430M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:13:25.519 430M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:25.524 430M / 8437M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:25.524 430M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:25.546 430M / 8437M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:13:25.546 430M / 8437M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:13:25.554 430M / 8437M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:13:25.559 430M / 8437M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 70 times 0:13:25.564 430M / 8437M INFO General (simplification.cpp : 495) After simplification: 0:13:25.564 430M / 8437M INFO General (simplification.cpp : 496) Average coverage = 641.452 0:13:25.569 430M / 8437M INFO General (simplification.cpp : 497) Total length = 12665872 0:13:25.574 430M / 8437M INFO General (simplification.cpp : 498) Median edge length: 17429 0:13:25.574 430M / 8437M INFO General (simplification.cpp : 499) Edges: 37387 0:13:25.574 430M / 8437M INFO General (simplification.cpp : 500) Vertices: 30180 0:13:25.574 430M / 8437M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:13:25.577 430M / 8437M INFO General (read_converter.cpp : 107) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K33/simplified_contigs 0:13:25.589 433M / 8437M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:13:25.602 433M / 8437M INFO General (binary_converter.cpp : 111) 18696 reads written 0:13:25.930 430M / 8437M INFO General (pipeline.cpp : 287) SPAdes finished 0:13:25.980 1M / 8437M INFO General (main.cpp : 136) Assembling time: 0 hours 13 minutes 26 seconds ===== K33 finished. ===== K55 started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades-core /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/configs/config.info 0:00:00.000 1M / 33M INFO General (main.cpp : 99) Loaded config from /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/configs/config.info 0:00:00.001 1M / 33M INFO General (memory_limit.cpp : 54) Memory limit set to 250 Gb 0:00:00.001 1M / 33M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.4, git revision 1a5332e5608a073a9d28a6d0e30836f38dcc5613 0:00:00.001 1M / 33M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.001 1M / 33M INFO General (main.cpp : 109) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/dataset.info) with K=55 0:00:00.001 1M / 33M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.001 1M / 33M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.001 1M / 33M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.001 1M / 33M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:00:00.001 1M / 33M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 0:00:00.001 1M / 33M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.004 1M / 33M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.006 1M / 33M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.008 1M / 33M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:00.008 1M / 33M INFO General (construction.cpp : 118) Contigs from previous K will be used: /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K33/simplified_contigs 0:00:00.096 2M / 33M INFO General (construction.cpp : 153) Max read length 149 0:00:00.096 2M / 33M INFO General (construction.cpp : 159) Average read length 80.1405 0:00:00.096 2M / 33M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:00.096 2M / 33M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 160 files using 16 threads. This might take a while. 0:00:00.101 2M / 33M INFO General (file_limit.hpp : 42) Open file limit set to 1024 0:00:00.101 2M / 33M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.20831 Gb 0:00:00.101 2M / 33M INFO General (kmer_splitter.hpp : 101) Using cell size of 209715 0:00:31.784 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 53436438 reads 0:00:58.134 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 79682119 reads 0:01:24.804 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 105726165 reads 0:01:52.140 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 131879852 reads 0:02:24.351 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 158218790 reads 0:02:55.576 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 184423217 reads 0:03:29.043 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 210729100 reads 0:03:58.991 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 236869743 reads 0:04:25.873 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 262929326 reads 0:04:55.746 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 289078807 reads 0:05:23.207 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 315640287 reads 0:05:50.082 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 339714462 reads 0:06:14.743 9602M / 9602M INFO General (kmer_splitters.hpp : 125) Processed 346524914 reads 0:06:14.762 2M / 8005M INFO General (kmer_splitters.hpp : 131) Used 346524914 reads 0:06:15.212 2M / 8005M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:06:23.291 2M / 8005M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 49267602 kmers in total. 0:06:23.293 2M / 8005M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:06:23.545 2M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:06:23.545 2M / 8005M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 160 files using 16 threads. This might take a while. 0:06:23.549 2M / 8005M INFO General (file_limit.hpp : 42) Open file limit set to 1024 0:06:23.549 2M / 8005M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.20831 Gb 0:06:23.549 2M / 8005M INFO General (kmer_splitter.hpp : 101) Using cell size of 209715 0:06:57.510 9602M / 9602M INFO General (kmer_splitters.hpp : 194) Processed 49267602 kmers 0:06:57.510 9602M / 9602M INFO General (kmer_splitters.hpp : 199) Used 49267602 kmers. 0:06:57.512 2M / 8005M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:07:05.323 2M / 8005M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 49147653 kmers in total. 0:07:05.323 2M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:07:06.042 39M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 49147653 kmers, 35617328 bytes occupied (5.7976 bits per kmer). 0:07:06.042 39M / 8005M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:07:14.635 87M / 8005M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:07:16.478 87M / 8005M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:07:16.658 87M / 8005M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:07:16.819 87M / 8005M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:07:19.388 257M / 8005M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3540703 sequences extracted 0:07:20.744 257M / 8005M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:07:21.288 257M / 8005M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:07:21.435 257M / 8005M INFO General (debruijn_graph_constructor: 487) Total 7081406 edges to create 0:07:21.435 530M / 8005M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:07:24.782 642M / 8005M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:07:24.851 642M / 8005M INFO General (debruijn_graph_constructor: 493) Sorting done 0:07:24.906 674M / 8005M INFO General (debruijn_graph_constructor: 503) Total 3420754 vertices to create 0:07:24.906 991M / 8005M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:07:28.040 792M / 8005M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:07:28.040 792M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:07:28.513 829M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 49267602 kmers, 35704368 bytes occupied (5.79762 bits per kmer). 0:07:28.619 1017M / 8005M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:08:48.960 1017M / 8005M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:08:51.228 1017M / 8005M INFO General (coverage_filling.hpp : 82) Processed 7081402 edges 0:08:51.763 785M / 8005M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:08:52.228 866M / 8005M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 37 0:08:52.243 785M / 8005M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 91 0:08:52.243 785M / 8005M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 93. Coverage mad: 41.5128 0:08:52.259 785M / 8005M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:08:52.429 866M / 8005M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:08:52.747 866M / 8005M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:08:53.926 866M / 8005M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:08:56.299 866M / 8005M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:08:59.566 866M / 8005M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:09:03.517 866M / 8005M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 246.718. Fitted coverage std. dev: 181.865 0:09:03.517 866M / 8005M WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 3 0:09:03.519 866M / 8005M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:09:03.519 866M / 8005M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 80 0:09:03.519 866M / 8005M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 80 0:09:03.519 866M / 8005M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 10336561 0:09:03.524 785M / 8005M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 246.718 0:09:03.524 785M / 8005M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 80 0:09:03.525 785M / 8005M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:09:03.525 785M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 0:09:03.529 794M / 8005M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:09:03.909 830M / 8005M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 1807665 out of 7081402, length: 34743600 0:09:04.129 855M / 8005M INFO General (edge_index.hpp : 167) Using small index (max_id = 7116816) 0:09:04.356 855M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:09:05.522 875M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 26807478 kmers, 19362824 bytes occupied (5.77834 bits per kmer). 0:09:05.649 1083M / 8005M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:09:06.332 1083M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:09:06.334 1083M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:09:06.334 1083M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:09:06.334 1083M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:09:06.334 1083M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:09:06.334 1083M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:09:06.335 1083M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:09:06.379 1083M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4204400 reads 0:09:06.463 1058M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 6435597 reads processed 0:09:06.465 1022M / 8005M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:09:06.465 1022M / 8005M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:09:11.306 1022M / 8005M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:09:11.418 1022M / 8005M INFO General (gap_closer.cpp : 456) Gap closer done 0:09:11.820 1058M / 8005M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 1807665 out of 7081402, length: 34743600 0:09:15.294 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:09:15.442 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:09:15.462 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:09:15.601 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:09:15.739 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:09:15.799 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:09:16.042 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:09:19.484 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:09:24.003 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:09:34.590 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:09:55.644 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 0:10:38.185 1059M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 67200000 reads 0:11:00.403 1064M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 79693563 reads processed 0:11:00.520 806M / 8005M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:11:00.521 806M / 8005M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:11:06.429 806M / 8005M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 86 gaps after checking 13659 candidates 0:11:06.547 806M / 8005M INFO General (gap_closer.cpp : 456) Gap closer done 0:11:06.568 785M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:11:06.568 785M / 8005M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 0:11:06.568 785M / 8005M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:11:06.568 785M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 0:11:06.725 785M / 8005M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 1 times 0:11:06.725 785M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 0:11:14.327 722M / 8005M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 1294405 times 0:11:14.335 722M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 0:11:16.495 725M / 8005M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 207035 times 0:11:16.501 725M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 0:11:16.857 720M / 8005M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 205309 times 0:11:16.859 686M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:11:16.859 686M / 8005M INFO General (simplification.cpp : 368) Graph simplification started 0:11:16.859 686M / 8005M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:11:16.859 686M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:11:16.859 686M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:16.987 685M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 22814 times 0:11:16.989 685M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:26.313 860M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 31700 times 0:11:26.314 860M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:26.892 860M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 60819 times 0:11:26.895 860M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:11:26.895 860M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:26.938 858M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2180 times 0:11:26.938 858M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:29.566 902M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 9324 times 0:11:29.567 902M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:29.639 901M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 7862 times 0:11:29.639 901M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:11:29.639 901M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:29.644 901M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 143 times 0:11:29.644 901M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:29.931 905M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 883 times 0:11:29.933 905M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:29.956 905M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 2531 times 0:11:29.957 905M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:11:29.957 905M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:29.959 905M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 35 times 0:11:29.959 905M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.044 906M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 236 times 0:11:30.045 906M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.056 906M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1254 times 0:11:30.058 906M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:11:30.058 906M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:30.058 906M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 12 times 0:11:30.059 906M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.092 906M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 87 times 0:11:30.093 906M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.100 906M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 754 times 0:11:30.100 906M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:11:30.100 906M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:30.101 906M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 12 times 0:11:30.101 906M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.118 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 55 times 0:11:30.118 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.123 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 496 times 0:11:30.123 907M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:11:30.124 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:30.124 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 5 times 0:11:30.124 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.131 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 25 times 0:11:30.132 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.136 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 371 times 0:11:30.136 907M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:11:30.136 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:30.136 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 0:11:30.136 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.141 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 17 times 0:11:30.141 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.144 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 260 times 0:11:30.145 907M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:11:30.145 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:30.145 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:11:30.145 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.148 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 11 times 0:11:30.148 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.151 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 214 times 0:11:30.151 907M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:11:30.151 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:30.151 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:11:30.152 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.155 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 11 times 0:11:30.155 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.157 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 158 times 0:11:30.158 907M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:11:30.158 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:30.166 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 21 times 0:11:30.166 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.183 907M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 9 times 0:11:30.184 907M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.192 905M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:11:30.192 905M / 8005M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 12 0:11:30.192 905M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:11:30.192 905M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:11:30.192 905M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:11:30.192 905M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:11:30.192 905M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:11:30.192 905M / 8005M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:11:30.203 904M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 0:11:30.209 913M / 8005M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:11:30.221 913M / 8005M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 3384 out of 20038, length: 7811112 0:11:30.222 913M / 8005M INFO General (edge_index.hpp : 167) Using small index (max_id = 7116816) 0:11:30.256 913M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:11:30.493 918M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6163481 kmers, 4452400 bytes occupied (5.77907 bits per kmer). 0:11:30.511 966M / 8005M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:11:30.669 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:11:30.677 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:11:30.677 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:11:30.677 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:11:30.677 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:11:30.677 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:11:30.678 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:11:30.734 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4206597 reads 0:11:30.808 966M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 6435597 reads processed 0:11:30.811 966M / 8005M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:11:30.811 966M / 8005M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:11:30.830 966M / 8005M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:11:30.841 966M / 8005M INFO General (gap_closer.cpp : 456) Gap closer done 0:11:30.861 966M / 8005M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 3384 out of 20038, length: 7811112 0:11:33.773 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:11:34.433 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:11:34.444 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:11:34.514 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:11:34.562 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:11:34.679 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:11:34.916 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:11:38.252 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:11:42.556 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:11:53.924 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:12:15.044 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 0:12:57.374 966M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 67200000 reads 0:13:20.149 966M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 79693563 reads processed 0:13:20.158 914M / 8005M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:13:20.158 914M / 8005M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:13:20.190 914M / 8005M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 1 gaps after checking 172 candidates 0:13:20.203 914M / 8005M INFO General (gap_closer.cpp : 456) Gap closer done 0:13:20.204 904M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:13:20.205 904M / 8005M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:13:20.205 904M / 8005M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:13:20.205 904M / 8005M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:13:20.205 904M / 8005M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:13:20.205 904M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:20.219 904M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:20.219 904M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:20.244 904M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:13:20.244 904M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:20.255 904M / 8005M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:13:20.255 904M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:13:20.275 904M / 8005M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:13:20.275 904M / 8005M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:13:20.286 904M / 8005M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:13:20.297 904M / 8005M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 108 times 0:13:20.307 904M / 8005M INFO General (simplification.cpp : 495) After simplification: 0:13:20.308 904M / 8005M INFO General (simplification.cpp : 496) Average coverage = 392.645 0:13:20.317 904M / 8005M INFO General (simplification.cpp : 497) Total length = 12594118 0:13:20.327 904M / 8005M INFO General (simplification.cpp : 498) Median edge length: 24074 0:13:20.327 904M / 8005M INFO General (simplification.cpp : 499) Edges: 19820 0:13:20.328 904M / 8005M INFO General (simplification.cpp : 500) Vertices: 17140 0:13:20.328 904M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 0:13:20.328 904M / 8005M INFO General (graph_pack.cpp : 67) Index refill 0:13:20.328 904M / 8005M INFO General (edge_index.hpp : 156) Using small index (max_id = 7116816) 0:13:20.397 904M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:13:20.814 914M / 8005M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12594118 kmers, 9099158 bytes occupied (5.77994 bits per kmer). 0:13:20.879 1014M / 8005M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 0:13:21.118 1014M / 8005M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 4790508 kmers to process 0:13:22.126 1014M / 8005M INFO General (graph_pack.cpp : 79) Normalizing done 0:13:22.127 1014M / 8005M INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 0:13:22.880 1015M / 8005M INFO General (mismatch_correction.cpp : 192) Total 9456 edges (out of 19820) with 197176 potential mismatch positions (20.8519 positions per edge) 0:13:22.880 1015M / 8005M INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 0:13:22.929 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:13:22.929 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:13:22.929 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:13:22.930 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:13:22.930 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:13:22.930 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:13:22.944 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:13:22.953 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:13:22.998 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:13:23.072 1015M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:13:23.247 1016M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 26618240 reads processed 0:13:24.109 1020M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:13:24.117 1025M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:13:24.122 1029M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:13:24.135 1034M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:13:24.145 1038M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:13:24.149 1043M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:13:24.194 1048M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:13:24.936 1050M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:13:25.823 1056M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:13:28.202 1064M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:13:32.984 1073M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 0:13:41.959 1085M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 67200000 reads 0:13:59.931 1099M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 134400000 reads 0:14:36.032 1106M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 268600000 reads 0:14:55.000 1246M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 319869282 reads processed 0:14:55.156 1030M / 8005M INFO General (mismatch_correction.cpp : 395) All edges processed 0:14:55.162 1014M / 8005M INFO General (mismatch_correction.cpp : 450) Corrected 12 nucleotides 0:14:55.163 1014M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:14:55.163 1014M / 8005M INFO General (contig_output.hpp : 16) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/before_rr.fasta 0:14:55.446 1014M / 8005M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/assembly_graph_after_simplification.gfa 0:14:55.728 1014M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 0:14:55.832 1021M / 8005M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 4791358 kmers to process 0:14:56.864 1021M / 8005M INFO General (graph_pack.cpp : 79) Normalizing done 0:14:56.873 1021M / 8005M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 24074 0:14:56.873 1021M / 8005M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 0:14:56.873 1021M / 8005M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 0:14:56.995 1293M / 8005M INFO General (pair_info_count.cpp : 44) Mapping PE reads shorter than K with BWA-mem mapper 0:14:57.219 1330M / 8005M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm 0:15:10.577 1318M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:15:10.986 1318M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:15:11.037 1318M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:15:11.062 1318M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:15:11.087 1318M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:15:11.115 1318M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:15:11.358 1318M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:15:18.674 1318M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4202300 reads 0:15:23.384 1318M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 6435597 reads processed 0:15:23.477 1293M / 8005M INFO General (pair_info_count.cpp : 220) Edge pairs: 13071 0:15:23.478 1293M / 8005M INFO General (pair_info_count.cpp : 222) 2242223 paired reads (34.8409% of all) aligned to long edges 0:15:23.480 1021M / 8005M INFO General (pair_info_count.cpp : 369) Insert size = 116.48, deviation = 64.1822, left quantile = 53, right quantile = 205, read length = 38 0:15:23.490 1021M / 8005M INFO General (pair_info_count.cpp : 390) Filtering data for library #0 0:15:23.496 1021M / 8005M INFO General (pair_info_count.cpp : 44) Mapping PE reads shorter than K with BWA-mem mapper 0:15:23.720 1058M / 8005M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm 0:15:36.168 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:15:36.174 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:15:36.205 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:15:36.220 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:15:36.230 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:15:36.234 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:15:36.398 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:15:43.684 1058M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4202200 reads 0:15:48.873 1046M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 6435597 reads processed 0:15:48.875 1021M / 8005M INFO General (pair_info_count.cpp : 402) Mapping library #0 0:15:48.875 1021M / 8005M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 0:15:48.875 1021M / 8005M INFO General (pair_info_count.cpp : 299) Left insert size quantile 53, right insert size quantile 205, filtering threshold 2, rounding threshold 0 0:15:48.889 1030M / 8005M INFO General (pair_info_count.cpp : 44) Mapping PE reads shorter than K with BWA-mem mapper 0:15:49.133 1067M / 8005M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm 0:16:01.950 1055M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:16:02.432 1055M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:16:02.462 1055M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:16:02.476 1056M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:16:02.523 1056M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:16:02.540 1056M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:16:02.644 1056M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:16:09.947 1056M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4204500 reads 0:16:12.651 1058M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 6435597 reads processed 0:16:12.662 1025M / 8005M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #1 0:16:12.662 1025M / 8005M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 0:16:12.805 1297M / 8005M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:16:13.739 1297M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:16:13.763 1297M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:16:13.791 1297M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:16:13.820 1297M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:16:13.849 1297M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:16:13.877 1297M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:16:14.049 1297M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:16:14.873 1297M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:16:16.030 1298M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:16:18.976 1298M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:16:24.521 1298M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 0:16:35.394 1298M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 67200000 reads 0:16:43.481 1297M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 79693563 reads processed 0:16:43.601 1297M / 8005M INFO General (pair_info_count.cpp : 220) Edge pairs: 1700885 0:16:43.602 1297M / 8005M INFO General (pair_info_count.cpp : 222) 19808271 paired reads (24.8555% of all) aligned to long edges 0:16:43.604 1025M / 8005M INFO General (pair_info_count.cpp : 369) Insert size = 111.366, deviation = 58.2701, left quantile = 62, right quantile = 187, read length = 149 0:16:43.610 1025M / 8005M WARN General (pair_info_count.cpp : 376) Estimated mean insert size 111.366 is very small compared to read length 149 0:16:43.612 1030M / 8005M INFO General (pair_info_count.cpp : 390) Filtering data for library #1 0:16:43.616 1030M / 8005M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:16:44.578 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:16:44.639 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:16:44.645 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:16:44.657 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:16:44.664 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:16:44.665 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:16:44.845 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:16:45.621 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:16:46.807 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:16:49.623 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:16:55.081 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 0:17:05.929 1030M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 67200000 reads 0:17:13.374 1030M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 79693563 reads processed 0:17:13.374 1030M / 8005M INFO General (pair_info_count.cpp : 402) Mapping library #1 0:17:13.375 1030M / 8005M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 0:17:13.375 1030M / 8005M INFO General (pair_info_count.cpp : 299) Left insert size quantile 62, right insert size quantile 187, filtering threshold 2, rounding threshold 0 0:17:13.395 1039M / 8005M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:17:14.557 1042M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:17:14.590 1045M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:17:14.653 1048M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:17:14.660 1051M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:17:14.667 1054M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:17:14.689 1057M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:17:14.780 1060M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:17:15.972 1065M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:17:17.381 1067M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:17:21.376 1073M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:17:29.211 1080M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 0:17:44.478 1085M / 8005M INFO General (sequence_mapper_notifier.h: 77) Processed 67200000 reads 0:17:51.502 1284M / 8005M INFO General (sequence_mapper_notifier.h: 95) Total 79693563 reads processed 0:17:51.517 1270M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 0:17:51.517 1270M / 8005M INFO General (distance_estimation.cpp : 179) Processing library #0 0:17:51.517 1270M / 8005M INFO General (distance_estimation.cpp : 150) Weight Filter Done 0:17:51.517 1270M / 8005M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:17:51.694 1270M / 8005M INFO General (distance_estimation.cpp : 37) Filtering info 0:17:51.695 1270M / 8005M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 22778 0:17:51.710 1269M / 8005M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 6102 0:17:51.710 1269M / 8005M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:17:51.711 1269M / 8005M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:17:51.711 1269M / 8005M INFO General (distance_estimation.cpp : 160) Improving paired information 0:17:51.755 1269M / 8005M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 2839; contradictional = 18 0:17:51.805 1269M / 8005M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 2004; contradictional = 0 0:17:51.806 1269M / 8005M INFO General (distance_estimation.cpp : 104) Filling scaffolding index 0:17:51.806 1269M / 8005M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:17:51.981 1269M / 8005M INFO General (distance_estimation.cpp : 37) Filtering info 0:17:51.982 1269M / 8005M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 20507 0:17:51.992 1270M / 8005M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 20507 0:17:51.992 1269M / 8005M INFO General (distance_estimation.cpp : 186) Clearing raw paired index 0:17:51.995 1265M / 8005M INFO General (distance_estimation.cpp : 179) Processing library #1 0:17:51.995 1265M / 8005M INFO General (distance_estimation.cpp : 150) Weight Filter Done 0:17:51.995 1265M / 8005M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:18:06.274 1475M / 8005M INFO General (distance_estimation.cpp : 37) Filtering info 0:18:06.281 1475M / 8005M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 13959920 0:18:09.107 1310M / 8005M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 630610 0:18:09.108 1294M / 8005M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:18:09.244 1294M / 8005M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:18:09.245 1294M / 8005M INFO General (distance_estimation.cpp : 160) Improving paired information 0:18:10.728 1336M / 8005M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 445414; contradictional = 850 0:18:13.487 1355M / 8005M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 195399; contradictional = 0 0:18:13.499 1355M / 8005M INFO General (distance_estimation.cpp : 104) Filling scaffolding index 0:18:13.500 1355M / 8005M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:18:28.693 1361M / 8005M INFO General (distance_estimation.cpp : 37) Filtering info 0:18:28.694 1361M / 8005M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 112415 0:18:28.726 1363M / 8005M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 112415 0:18:28.726 1361M / 8005M INFO General (distance_estimation.cpp : 186) Clearing raw paired index 0:18:28.918 1116M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 0:18:28.928 1116M / 8005M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 0:18:28.929 1116M / 8005M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 0:18:30.110 1116M / 8005M INFO General (coverage_uniformity_analyz: 25) genomic coverage is 266.659 calculated of length 11969727 0:18:30.122 1116M / 8005M WARN General (launcher.cpp : 178) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option. 0:18:30.168 1156M / 8005M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 0:18:30.169 1156M / 8005M INFO General (extenders_logic.cpp : 334) Estimated coverage of library #0 is 14.3028 0:18:30.170 1156M / 8005M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 15770 0:18:30.170 1157M / 8005M INFO General (extenders_logic.cpp : 334) Estimated coverage of library #0 is 14.3028 0:18:30.171 1157M / 8005M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 15770 0:18:30.187 1159M / 8005M INFO General (extenders_logic.cpp : 334) Estimated coverage of library #1 is 378.342 0:18:30.187 1159M / 8005M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 1911386 0:18:30.188 1161M / 8005M INFO General (extenders_logic.cpp : 334) Estimated coverage of library #1 is 378.342 0:18:30.188 1161M / 8005M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 1911386 0:18:30.198 1163M / 8005M INFO General (extenders_logic.cpp : 543) Using 2 paired-end libraries 0:18:30.198 1163M / 8005M INFO General (extenders_logic.cpp : 544) Using 2 paired-end scaffolding libraries 0:18:30.198 1163M / 8005M INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 0:18:30.198 1163M / 8005M INFO General (launcher.cpp : 447) Total number of extenders is 6 0:18:30.198 1163M / 8005M INFO General (path_extenders.cpp : 36) Processed 0 paths from 9789 (0%) 0:18:30.339 1167M / 8005M INFO General (path_extenders.cpp : 34) Processed 128 paths from 9789 (1%) 0:18:30.404 1170M / 8005M INFO General (path_extenders.cpp : 34) Processed 256 paths from 9789 (2%) 0:18:30.471 1174M / 8005M INFO General (path_extenders.cpp : 34) Processed 512 paths from 9789 (5%) 0:18:30.574 1179M / 8005M INFO General (path_extenders.cpp : 36) Processed 979 paths from 9789 (10%) 0:18:30.582 1179M / 8005M INFO General (path_extenders.cpp : 34) Processed 1024 paths from 9789 (10%) 0:18:30.676 1186M / 8005M INFO General (path_extenders.cpp : 36) Processed 1958 paths from 9789 (20%) 0:18:30.682 1186M / 8005M INFO General (path_extenders.cpp : 34) Processed 2048 paths from 9789 (20%) 0:18:30.739 1191M / 8005M INFO General (path_extenders.cpp : 36) Processed 2937 paths from 9789 (30%) 0:18:30.981 1200M / 8005M INFO General (path_extenders.cpp : 36) Processed 3916 paths from 9789 (40%) 0:18:31.026 1201M / 8005M INFO General (path_extenders.cpp : 34) Processed 4096 paths from 9789 (41%) 0:18:31.184 1206M / 8005M INFO General (path_extenders.cpp : 36) Processed 4895 paths from 9789 (50%) 0:18:31.336 1209M / 8005M INFO General (path_extenders.cpp : 36) Processed 5874 paths from 9789 (60%) 0:18:31.461 1212M / 8005M INFO General (path_extenders.cpp : 36) Processed 6853 paths from 9789 (70%) 0:18:31.536 1214M / 8005M INFO General (path_extenders.cpp : 36) Processed 7832 paths from 9789 (80%) 0:18:31.570 1215M / 8005M INFO General (path_extenders.cpp : 34) Processed 8192 paths from 9789 (83%) 0:18:31.603 1215M / 8005M INFO General (path_extenders.cpp : 36) Processed 8811 paths from 9789 (90%) 0:18:31.637 1216M / 8005M INFO General (launcher.cpp : 250) Finalizing paths 0:18:31.637 1216M / 8005M INFO General (launcher.cpp : 252) Deduplicating paths 0:18:31.758 1204M / 8005M INFO General (launcher.cpp : 256) Paths deduplicated 0:18:31.758 1204M / 8005M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 0:18:31.759 1204M / 8005M INFO PEResolver (pe_resolver.cpp : 63) Sorting paths 0:18:31.760 1204M / 8005M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 0:18:31.760 1204M / 8005M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 0:18:31.884 1204M / 8005M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 0:18:32.013 1204M / 8005M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 0:18:32.025 1215M / 8005M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 0:18:32.039 1203M / 8005M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 0:18:32.056 1220M / 8005M INFO General (launcher.cpp : 273) Paths finalized 0:18:32.056 1220M / 8005M INFO General (launcher.cpp : 454) Closing gaps in paths 0:18:32.077 1248M / 8005M INFO General (launcher.cpp : 484) Gap closing completed 0:18:32.081 1249M / 8005M INFO General (launcher.cpp : 302) Traversing tandem repeats 0:18:32.117 1249M / 8005M INFO General (launcher.cpp : 312) Traversed 10 loops 0:18:32.118 1249M / 8005M INFO General (launcher.cpp : 250) Finalizing paths 0:18:32.118 1249M / 8005M INFO General (launcher.cpp : 252) Deduplicating paths 0:18:32.121 1249M / 8005M INFO General (launcher.cpp : 256) Paths deduplicated 0:18:32.121 1249M / 8005M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 0:18:32.121 1249M / 8005M INFO PEResolver (pe_resolver.cpp : 63) Sorting paths 0:18:32.123 1249M / 8005M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 0:18:32.123 1249M / 8005M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 0:18:32.130 1249M / 8005M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 0:18:32.137 1249M / 8005M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 0:18:32.138 1250M / 8005M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 0:18:32.140 1249M / 8005M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 0:18:32.151 1250M / 8005M INFO General (launcher.cpp : 273) Paths finalized 0:18:32.152 1250M / 8005M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 0:18:32.193 1144M / 8005M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:18:32.194 1144M / 8005M INFO General (contig_output.hpp : 16) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/before_rr.fasta 0:18:32.512 1144M / 8005M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/assembly_graph_with_scaffolds.gfa 0:18:32.596 1144M / 8005M INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/assembly_graph.fastg 0:18:33.161 1144M / 8005M INFO General (contig_output_stage.cpp : 196) Breaking scaffolds 0:18:33.243 1192M / 8005M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/final_contigs.fasta 0:18:33.466 1192M / 8005M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/final_contigs.paths 0:18:33.652 1162M / 8005M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/scaffolds.fasta 0:18:33.990 1162M / 8005M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/scaffolds.paths 0:18:34.118 1162M / 8005M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 0:18:34.386 1144M / 8005M INFO General (pipeline.cpp : 287) SPAdes finished 0:18:35.473 1M / 8005M INFO General (main.cpp : 136) Assembling time: 0 hours 18 minutes 35 seconds ===== K55 finished. ===== Copy files started. == Running: /users/marinovg/miniconda3/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/scripts/copy_files.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/before_rr.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/before_rr.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/assembly_graph_after_simplification.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/assembly_graph_after_simplification.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/final_contigs.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/contigs.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/first_pe_contigs.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/first_pe_contigs.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/strain_graph.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/strain_graph.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/scaffolds.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/scaffolds.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/scaffolds.paths /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/scaffolds.paths /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/assembly_graph_with_scaffolds.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/assembly_graph_with_scaffolds.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/assembly_graph.fastg /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/assembly_graph.fastg /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/K55/final_contigs.paths /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/contigs.paths ===== Copy files finished. ===== Assembling finished. ===== Breaking scaffolds started. == Running: /users/marinovg/miniconda3/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/scaffolds.fasta --misc_dir /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/misc --threshold_for_breaking_scaffolds 3 ===== Breaking scaffolds finished. ===== Terminate started. ===== Terminate finished. * Corrected reads are in /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/corrected/ * Assembled contigs are in /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/contigs.fasta * Assembled scaffolds are in /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/scaffolds.fasta * Paths in the assembly graph corresponding to the contigs are in /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/scaffolds.paths * Assembly graph is in /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/assembly_graph.fastg * Assembly graph in GFA format is in /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 0:12:57.088 671M / 9147M WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 5 * 0:13:10.364 601M / 8437M WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 4 * 0:09:03.517 866M / 8005M WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 3 * 0:16:43.610 1025M / 8005M WARN General (pair_info_count.cpp : 376) Estimated mean insert size 111.366 is very small compared to read length 149 * 0:18:30.122 1116M / 8005M WARN General (launcher.cpp : 178) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option. ======= Warnings saved to /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/warnings.log SPAdes log can be found here: /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2-Illumina-only/spades.log Thank you for using SPAdes!