/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/tophat -G /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.gtf --transcriptome-index /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24 -p 16 -o /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome ./filtered_400_GTCCGC_L004_R1_trimmed.fastq.gz
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/gtf_juncs /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.gff  > /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.juncs
#>prep_reads:
/usr/local/bioinformatics/tophat-2.0.13.OSX_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 /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/ --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 --gtf-annotations /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.gff --gtf-juncs /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.juncs --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/prep_reads.info --index-outfile=/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.bam.index --sam-header=/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome_genome.bwt.samheader.sam --outfile=/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.bam ./filtered_400_GTCCGC_L004_R1_trimmed.fastq.gz
#>map_start:
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/bam2fastx --all /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.bam|/usr/local/bioinformatics/bowtie2/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 /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24 -|/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/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 /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.bwt.samheader.sam - - /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.bam | /usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/map2gtf --sam-header /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome_genome.bwt.samheader.sam /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.fa.tlst - /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g.bam > /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/logs/m2g_left_kept_reads.out
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/bam2fastx --all /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.bam|/usr/local/bioinformatics/bowtie2/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 /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome -|/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/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 /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.mapped.bam.index --sam-header /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome_genome.bwt.samheader.sam - /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.mapped.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um_unmapped.bam
#>map_segments:
#>find_juncs:
/usr/local/bioinformatics/tophat-2.0.13.OSX_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 /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/ --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 --gtf-annotations /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.gff --gtf-juncs /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.juncs --no-closure-search --no-microexon-search --sam-header /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome_genome.bwt.samheader.sam --ium-reads /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um_unmapped.bam /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome.fa /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment.juncs /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment.insertions /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment.deletions /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment.fusions /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.mapped.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.mapped.bam
#>juncs_db:
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/juncs_db 3 25 /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.juncs,/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment.juncs /dev/null /dev/null /dev/null /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome.fa > /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs.fa
/usr/local/bioinformatics/bowtie2/bowtie2-build /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs.fa /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs
#>map2juncs:
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/bam2fastx --all /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um_unmapped.bam|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 16 --sam-no-hd -x /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs -|/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/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 /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um_unmapped.to_spliced.bam.index --sam-header /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs.bwt.samheader.sam - /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um_unmapped.to_spliced.bam
/usr/local/bioinformatics/tophat-2.0.13.OSX_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 /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/ --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 --gtf-annotations /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.gff --gtf-juncs /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.juncs --no-closure-search --no-microexon-search --sam-header /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.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 /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome.fa /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.juncs,/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment.juncs /dev/null /dev/null /dev/null /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.candidates.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.mapped.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um_unmapped.to_spliced.bam
#>tophat_reports:
/usr/local/bioinformatics/tophat-2.0.13.OSX_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 /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/ --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 --gtf-annotations /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.gff --gtf-juncs /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.juncs --no-closure-search --no-microexon-search --sam-header /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/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 /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome.fa /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/junctions.bed /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/insertions.bed /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/deletions.bed /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/fusions.out /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g.bam,/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.mapped.bam,/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um.candidates.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.bam
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits0.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits0_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits1.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits1_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits2.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits2_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits3.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits3_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits4.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits4_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits5.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits5_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits6.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits6_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits7.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits7_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits8.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits8_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits9.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits9_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits10.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits10_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits11.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits11_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits12.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits12_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits13.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits13_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits14.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits14_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits15.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits15_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 merge -f -h /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome_genome.bwt.samheader.sam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/accepted_hits.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits0_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits1_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits2_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits3_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits4_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits5_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits6_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits7_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits8_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits9_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits10_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits11_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits12_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits13_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits14_sorted.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/accepted_hits15_sorted.bam
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/bam_merge -Q --sam-header /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome_genome.bwt.samheader.sam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/unmapped.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_0.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_1.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_2.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_3.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_4.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_5.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_6.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_7.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_8.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_9.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_10.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_11.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_12.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_13.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_14.bam /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/unmapped_left_15.bam
#>alldone: