(-: Looking for fastq files...fastq files exist
(-: Aligning files matching /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/fastq/*_R*.fastq*
 to genome hg19 with site file none
(-: Created /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/splits and /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/aligned.
bwa mem -SP5M -t 20 /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bwa-indexes/all.fa /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/splits/reads_R1.fastq.gz /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/splits/reads_R2.fastq.gz > /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/splits/reads.fastq.gz.sam
(-:  Align of /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/splits/reads.fastq.gz.sam done successfully
(-: Finished sorting all sorted files into a single merge.
Not including fragment map
Start preprocess
Writing header
Writing body
...........
Writing footer

Finished preprocess

Calculating norms for zoom BP_2500000
Calculating norms for zoom BP_1000000
Calculating norms for zoom BP_500000
Calculating norms for zoom BP_250000
Calculating norms for zoom BP_100000
Calculating norms for zoom BP_50000
Calculating norms for zoom BP_25000
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Writing expected
Writing norms
Finished writing norms
Not including fragment map
Start preprocess
Writing header
Writing body
...........
Writing footer

Finished preprocess

Calculating norms for zoom BP_2500000
Calculating norms for zoom BP_1000000
Calculating norms for zoom BP_500000
Calculating norms for zoom BP_250000
Calculating norms for zoom BP_100000
Calculating norms for zoom BP_50000
Calculating norms for zoom BP_25000
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Writing expected
Writing norms
Finished writing norms
/oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/scripts/common/juicer_tools is post-processing Hi-C for hg19
Data read from /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/aligned/inter_30.hic.
Motifs read from /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/references/motif

ARROWHEAD:

Reading file: /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/aligned/inter_30.hic
Default settings for 5kb being used
25% 
50% 
75% 
100% 
3 domains written to file: /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/aligned/inter_30_contact_domains/5000_blocks.bedpe
Arrowhead complete

HiCCUPS:

GPUs are not installed so HiCCUPs cannot be run

(-: Postprocessing successfully completed, maps too sparse to annotate or GPUs unavailable (-:
(-: Pipeline successfully completed (-:
Run cleanup.sh to remove the splits directory
Check /oak/stanford/groups/akundaje/marinovg/papers/2021_Haloferax-chromatin/2021-09-14-Hi-C-rerun/juicer-H.volcanii_WT_stationary-pooled-rerun/aligned for results