/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/dm3/FlyBase.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/dm3/TopHat-transcriptome-indexes/FlyBase -o S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3 S2-CAGE-Rep1-Celniker-ENCFF988NQG.fastq.gz
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/gtf_juncs /oak/stanford/groups/akundaje/marinovg/genomes/dm3/TopHat-transcriptome-indexes/FlyBase.gff  > S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/FlyBase.juncs
#>prep_reads:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p8 --gtf-annotations /oak/stanford/groups/akundaje/marinovg/genomes/dm3/TopHat-transcriptome-indexes/FlyBase.gff --gtf-juncs S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/FlyBase.juncs --no-closure-search --no-coverage-search --no-microexon-search --fastq --aux-outfile=S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/prep_reads.info --index-outfile=S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.bam.index --sam-header=S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/dm3_genome.bwt.samheader.sam --outfile=S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG.fastq.gz
#>map_start:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.bam|/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 60 -m 60 -S -p 8 --sam-nohead --max /dev/null /oak/stanford/groups/akundaje/marinovg/genomes/dm3/TopHat-transcriptome-indexes/FlyBase -|/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --bowtie1 --sam-header S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/FlyBase.bwt.samheader.sam - - S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.bam | /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/map2gtf --sam-header S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/dm3_genome.bwt.samheader.sam /oak/stanford/groups/akundaje/marinovg/genomes/dm3/TopHat-transcriptome-indexes/FlyBase.gff - S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g.bam > S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/logs/m2g_left_kept_reads.out
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.bam|/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 20 -m 20 -S -p 8 --sam-nohead --max /dev/null /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3 -|/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.mapped.bam.index --bowtie1 --sam-header S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/dm3_genome.bwt.samheader.sam - S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.mapped.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um_unmapped.bam
#>map_segments:
#>find_juncs:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p8 --gtf-annotations /oak/stanford/groups/akundaje/marinovg/genomes/dm3/TopHat-transcriptome-indexes/FlyBase.gff --gtf-juncs S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/FlyBase.juncs --no-closure-search --no-microexon-search --sam-header S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/dm3_genome.bwt.samheader.sam --ium-reads S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um_unmapped.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment.juncs S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment.insertions S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment.deletions S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment.fusions S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.mapped.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.mapped.bam
#>juncs_db:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/juncs_db 3 25 S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/FlyBase.juncs,S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment.juncs /dev/null /dev/null /dev/null /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa > S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment_juncs.fa
/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/bowtie-build S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment_juncs.fa S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment_juncs
#>map2juncs:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um_unmapped.bam|/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 8 --sam-nohead --max /dev/null S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment_juncs -|/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um_unmapped.to_spliced.bam.index --bowtie1 --sam-header S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment_juncs.bwt.samheader.sam - S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um_unmapped.to_spliced.bam
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p8 --gtf-annotations /oak/stanford/groups/akundaje/marinovg/genomes/dm3/TopHat-transcriptome-indexes/FlyBase.gff --gtf-juncs S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/FlyBase.juncs --no-closure-search --no-microexon-search --sam-header S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/dm3_genome.bwt.samheader.sam --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/FlyBase.juncs,S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/segment.juncs /dev/null /dev/null /dev/null S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.candidates.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.mapped.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um_unmapped.to_spliced.bam
#>tophat_reports:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p8 --gtf-annotations /oak/stanford/groups/akundaje/marinovg/genomes/dm3/TopHat-transcriptome-indexes/FlyBase.gff --gtf-juncs S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/FlyBase.juncs --no-closure-search --no-microexon-search --sam-header S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/dm3_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3.fa S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/junctions.bed S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/insertions.bed S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/deletions.bed S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/fusions.out S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g.bam,S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.mapped.bam,S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um.candidates.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits0.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits0_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits1.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits1_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits2.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits2_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits3.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits3_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits4.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits4_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits5.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits5_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits6.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits6_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits7.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits7_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools merge -f -h S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/dm3_genome.bwt.samheader.sam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/accepted_hits.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits0_sorted.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits1_sorted.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits2_sorted.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits3_sorted.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits4_sorted.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits5_sorted.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits6_sorted.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/accepted_hits7_sorted.bam
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam_merge -Q --sam-header S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/dm3_genome.bwt.samheader.sam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/unmapped.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/unmapped_left_0.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/unmapped_left_1.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/unmapped_left_2.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/unmapped_left_3.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/unmapped_left_4.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/unmapped_left_5.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/unmapped_left_6.bam S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/unmapped_left_7.bam
#>alldone: