/share/pkg.7/tophat/2.1.1/install/bin/tophat --no-coverage-search -o /scratch/7287270.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR8261775_1.fastq.gz SRR8261775_2.fastq.gz
/share/pkg.7/tophat/2.1.1/install/bin/gtf_juncs RefSeq_GeneBody.gtf  > /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs
#>prep_reads:
/share/pkg.7/tophat/2.1.1/install/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /scratch/7287270.1.linga/tophat2/ --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 -z gzip -p16 --inner-dist-mean -86 --inner-dist-std-dev 150 --gtf-annotations RefSeq_GeneBody.gtf --gtf-juncs /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --aux-outfile=/scratch/7287270.1.linga/tophat2/prep_reads.info --index-outfile=/scratch/7287270.1.linga/tophat2/tmp/%side%_kept_reads.bam.index --sam-header=/scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam --outfile=/scratch/7287270.1.linga/tophat2/tmp/%side%_kept_reads.bam SRR8261775_1.fastq.gz SRR8261775_2.fastq.gz
#>map_start:
/share/pkg.7/tophat/2.1.1/install/bin/gtf_to_fasta --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /scratch/7287270.1.linga/tophat2/ --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 -z gzip -p16 --inner-dist-mean -86 --inner-dist-std-dev 150 --gtf-annotations RefSeq_GeneBody.gtf --gtf-juncs /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand RefSeq_GeneBody.gtf Bowtie2Index/genome.fa /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.fa > /scratch/7287270.1.linga/tophat2/logs/g2f.out
/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2-build /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.fa /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody
/share/pkg.7/tophat/2.1.1/install/bin/bam2fastx --all /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.bam|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --sam-header /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.bwt.samheader.sam - - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.bam | /share/pkg.7/tophat/2.1.1/install/bin/map2gtf --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.fa.tlst - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g.bam > /scratch/7287270.1.linga/tophat2/logs/m2g_left_kept_reads.out
/share/pkg.7/tophat/2.1.1/install/bin/bam2fastx --all /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.bam|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --sam-header /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.bwt.samheader.sam - - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.bam | /share/pkg.7/tophat/2.1.1/install/bin/map2gtf --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.fa.tlst - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g.bam > /scratch/7287270.1.linga/tophat2/logs/m2g_right_kept_reads.out
/share/pkg.7/tophat/2.1.1/install/bin/bam2fastx --all /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.bam|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.mapped.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.mapped.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
#>map_segments:
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6_unmapped.bam
/share/pkg.7/tophat/2.1.1/install/bin/bam2fastx --all /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.bam|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.mapped.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.mapped.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
#>map_segments:
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5_unmapped.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x Bowtie2Index/genome -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6_unmapped.bam
#>find_juncs:
/share/pkg.7/tophat/2.1.1/install/bin/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /scratch/7287270.1.linga/tophat2/ --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 -z gzip -p16 --inner-dist-mean -86 --inner-dist-std-dev 150 --gtf-annotations RefSeq_GeneBody.gtf --gtf-juncs /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam --ium-reads /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5_unmapped.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6_unmapped.bam Bowtie2Index/genome.fa /scratch/7287270.1.linga/tophat2/tmp/segment.juncs /scratch/7287270.1.linga/tophat2/tmp/segment.insertions /scratch/7287270.1.linga/tophat2/tmp/segment.deletions /scratch/7287270.1.linga/tophat2/tmp/segment.fusions /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.mapped.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.mapped.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.bam
#>juncs_db:
/share/pkg.7/tophat/2.1.1/install/bin/juncs_db 3 25 /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs,/scratch/7287270.1.linga/tophat2/tmp/segment.juncs /dev/null /dev/null /dev/null Bowtie2Index/genome.fa > /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.fa
/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2-build /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.fa /scratch/7287270.1.linga/tophat2/tmp/segment_juncs
#>map2juncs:
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam
/share/pkg.7/tophat/2.1.1/install/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /scratch/7287270.1.linga/tophat2/ --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 -z gzip -p16 --inner-dist-mean -86 --inner-dist-std-dev 150 --gtf-annotations RefSeq_GeneBody.gtf --gtf-juncs /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_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 Bowtie2Index/genome.fa /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.bam /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs,/scratch/7287270.1.linga/tophat2/tmp/segment.juncs /scratch/7287270.1.linga/tophat2/tmp/segment.insertions /scratch/7287270.1.linga/tophat2/tmp/segment.deletions /dev/null /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.candidates.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.bam /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.to_spliced.bam
gzip -cd< /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.fq.z|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /scratch/7287270.1.linga/tophat2/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.to_spliced.bam.index --sam-header /scratch/7287270.1.linga/tophat2/tmp/segment_juncs.bwt.samheader.sam - /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.to_spliced.bam
/share/pkg.7/tophat/2.1.1/install/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /scratch/7287270.1.linga/tophat2/ --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 -z gzip -p16 --inner-dist-mean -86 --inner-dist-std-dev 150 --gtf-annotations RefSeq_GeneBody.gtf --gtf-juncs /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_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 Bowtie2Index/genome.fa /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.bam /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs,/scratch/7287270.1.linga/tophat2/tmp/segment.juncs /scratch/7287270.1.linga/tophat2/tmp/segment.insertions /scratch/7287270.1.linga/tophat2/tmp/segment.deletions /dev/null /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.candidates.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg1.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg2.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg3.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg4.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg5.to_spliced.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um_seg6.to_spliced.bam
#>tophat_reports:
/share/pkg.7/tophat/2.1.1/install/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /scratch/7287270.1.linga/tophat2/ --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 -z gzip -p16 --inner-dist-mean -86 --inner-dist-std-dev 150 --gtf-annotations RefSeq_GeneBody.gtf --gtf-juncs /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 --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 Bowtie2Index/genome.fa /scratch/7287270.1.linga/tophat2/junctions.bed /scratch/7287270.1.linga/tophat2/insertions.bed /scratch/7287270.1.linga/tophat2/deletions.bed /scratch/7287270.1.linga/tophat2/fusions.out /scratch/7287270.1.linga/tophat2/tmp/accepted_hits /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.mapped.bam,/scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.m2g_um.candidates /scratch/7287270.1.linga/tophat2/tmp/left_kept_reads.bam /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.mapped.bam,/scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.m2g_um.candidates /scratch/7287270.1.linga/tophat2/tmp/right_kept_reads.bam
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits0.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits0_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits1.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits1_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits2.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits2_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits3.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits3_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits4.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits4_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits5.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits5_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits6.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits6_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits7.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits7_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits8.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits8_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits9.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits9_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits10.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits10_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits11.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits11_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits12.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits12_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits13.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits13_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits14.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits14_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort /scratch/7287270.1.linga/tophat2/tmp/accepted_hits15.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits15_sorted
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 merge -f -h /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam /scratch/7287270.1.linga/tophat2/accepted_hits.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits0_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits1_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits2_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits3_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits4_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits5_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits6_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits7_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits8_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits9_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits10_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits11_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits12_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits13_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits14_sorted.bam /scratch/7287270.1.linga/tophat2/tmp/accepted_hits15_sorted.bam
/share/pkg.7/tophat/2.1.1/install/bin/bam_merge -Q --sam-header /scratch/7287270.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam /scratch/7287270.1.linga/tophat2/unmapped.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_0.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_0.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_1.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_1.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_2.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_2.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_3.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_3.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_4.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_4.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_5.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_5.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_6.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_6.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_7.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_7.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_8.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_8.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_9.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_9.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_10.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_10.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_11.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_11.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_12.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_12.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_13.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_13.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_14.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_14.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_left_15.bam /scratch/7287270.1.linga/tophat2/tmp/unmapped_right_15.bam
#>alldone: