/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome -o Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0 /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds CEHL_TM0f.36mers.fastq.gz
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/gtf_juncs /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome.gff  > Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/ --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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome.gff --gtf-juncs Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.juncs --no-closure-search --no-coverage-search --no-microexon-search --fastq --aux-outfile=Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/prep_reads.info --index-outfile=Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.bam.index --sam-header=Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.scaffolds_genome.bwt.samheader.sam --outfile=Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.bam CEHL_TM0f.36mers.fastq.gz
#>map_start:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome -|/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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.bwt.samheader.sam - - Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.bam | /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/map2gtf --sam-header Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.scaffolds_genome.bwt.samheader.sam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome.gff - Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g.bam > Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/logs/m2g_left_kept_reads.out
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -|/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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.mapped.bam.index --bowtie1 --sam-header Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.scaffolds_genome.bwt.samheader.sam - Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.mapped.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/ --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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome.gff --gtf-juncs Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.juncs --no-closure-search --no-microexon-search --sam-header Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.scaffolds_genome.bwt.samheader.sam --ium-reads Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um_unmapped.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment.juncs Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment.insertions Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment.deletions Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment.fusions Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.mapped.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.juncs,Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment.juncs /dev/null /dev/null /dev/null /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa > Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment_juncs.fa
/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/bowtie-build Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment_juncs.fa Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment_juncs
#>map2juncs:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um_unmapped.to_spliced.bam.index --bowtie1 --sam-header Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment_juncs.bwt.samheader.sam - Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/ --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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome.gff --gtf-juncs Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.juncs --no-closure-search --no-microexon-search --sam-header Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.scaffolds_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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.juncs,Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/segment.juncs /dev/null /dev/null /dev/null Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.candidates.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.mapped.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/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 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/ --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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome.gff --gtf-juncs Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.juncs --no-closure-search --no-microexon-search --sam-header Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.scaffolds_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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/junctions.bed Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/insertions.bed Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/deletions.bed Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/fusions.out Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g.bam,Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.mapped.bam,Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.m2g_um.candidates.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/left_kept_reads.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits0.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits0_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits1.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits1_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits2.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits2_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits3.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits3_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits4.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits4_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits5.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits5_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits6.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits6_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits7.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits7_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools merge -f -h Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.scaffolds_genome.bwt.samheader.sam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/accepted_hits.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits0_sorted.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits1_sorted.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits2_sorted.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits3_sorted.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits4_sorted.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits5_sorted.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits6_sorted.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/accepted_hits7_sorted.bam
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam_merge -Q --sam-header Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/aiptasia_genome.scaffolds_genome.bwt.samheader.sam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/unmapped.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/unmapped_left_0.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/unmapped_left_1.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/unmapped_left_2.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/unmapped_left_3.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/unmapped_left_4.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/unmapped_left_5.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/unmapped_left_6.bam Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/tmp/unmapped_left_7.bam
#>alldone: