/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/tophat -p 8 -o 2M /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel 2M_AGTCAA_L001_R1_001.fastq.gz
#>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 2M/ --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 -p8 --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=2M/prep_reads.info --index-outfile=2M/tmp/left_kept_reads.bam.index --sam-header=2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam --outfile=2M/tmp/left_kept_reads.bam 2M_AGTCAA_L001_R1_001.fastq.gz
#>map_start:
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/bam2fastx --all 2M/tmp/left_kept_reads.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 8 --sam-no-hd -x /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel -|/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 2M/tmp/left_kept_reads.mapped.bam.index --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam - 2M/tmp/left_kept_reads.mapped.bam 2M/tmp/left_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< 2M/tmp/left_kept_reads_seg1.fq.z|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel -|/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 2M/tmp/left_kept_reads_seg1.bam.index --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam - 2M/tmp/left_kept_reads_seg1.bam 2M/tmp/left_kept_reads_seg1_unmapped.bam
gzip -cd< 2M/tmp/left_kept_reads_seg2.fq.z|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel -|/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 2M/tmp/left_kept_reads_seg2.bam.index --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam - 2M/tmp/left_kept_reads_seg2.bam 2M/tmp/left_kept_reads_seg2_unmapped.bam
gzip -cd< 2M/tmp/left_kept_reads_seg3.fq.z|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel -|/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 2M/tmp/left_kept_reads_seg3.bam.index --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam - 2M/tmp/left_kept_reads_seg3.bam 2M/tmp/left_kept_reads_seg3_unmapped.bam
gzip -cd< 2M/tmp/left_kept_reads_seg4.fq.z|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel -|/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 2M/tmp/left_kept_reads_seg4.bam.index --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam - 2M/tmp/left_kept_reads_seg4.bam 2M/tmp/left_kept_reads_seg4_unmapped.bam
#>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 2M/ --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 -p8 --no-closure-search --no-coverage-search --no-microexon-search --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam --ium-reads 2M/tmp/left_kept_reads_seg1_unmapped.bam,2M/tmp/left_kept_reads_seg2_unmapped.bam,2M/tmp/left_kept_reads_seg3_unmapped.bam,2M/tmp/left_kept_reads_seg4_unmapped.bam /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel.fa 2M/tmp/segment.juncs 2M/tmp/segment.insertions 2M/tmp/segment.deletions 2M/tmp/segment.fusions 2M/tmp/left_kept_reads.bam 2M/tmp/left_kept_reads.mapped.bam 2M/tmp/left_kept_reads_seg1.bam,2M/tmp/left_kept_reads_seg2.bam,2M/tmp/left_kept_reads_seg3.bam,2M/tmp/left_kept_reads_seg4.bam
#>juncs_db:
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/juncs_db 3 26 2M/tmp/segment.juncs /dev/null /dev/null /dev/null /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel.fa > 2M/tmp/segment_juncs.fa
/usr/local/bioinformatics/bowtie2/bowtie2-build 2M/tmp/segment_juncs.fa 2M/tmp/segment_juncs
#>map2juncs:
gzip -cd< 2M/tmp/left_kept_reads_seg1.fq.z|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x 2M/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 2M/tmp/left_kept_reads_seg1.to_spliced.bam.index --sam-header 2M/tmp/segment_juncs.bwt.samheader.sam - 2M/tmp/left_kept_reads_seg1.to_spliced.bam
gzip -cd< 2M/tmp/left_kept_reads_seg2.fq.z|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x 2M/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 2M/tmp/left_kept_reads_seg2.to_spliced.bam.index --sam-header 2M/tmp/segment_juncs.bwt.samheader.sam - 2M/tmp/left_kept_reads_seg2.to_spliced.bam
gzip -cd< 2M/tmp/left_kept_reads_seg3.fq.z|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x 2M/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 2M/tmp/left_kept_reads_seg3.to_spliced.bam.index --sam-header 2M/tmp/segment_juncs.bwt.samheader.sam - 2M/tmp/left_kept_reads_seg3.to_spliced.bam
gzip -cd< 2M/tmp/left_kept_reads_seg4.fq.z|/usr/local/bioinformatics/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x 2M/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 2M/tmp/left_kept_reads_seg4.to_spliced.bam.index --sam-header 2M/tmp/segment_juncs.bwt.samheader.sam - 2M/tmp/left_kept_reads_seg4.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 2M/ --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 -p8 --no-closure-search --no-coverage-search --no-microexon-search --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_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/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel.fa 2M/tmp/left_kept_reads.bam 2M/tmp/segment.juncs 2M/tmp/segment.insertions 2M/tmp/segment.deletions /dev/null 2M/tmp/left_kept_reads.candidates.bam 2M/tmp/left_kept_reads_seg1.bam,2M/tmp/left_kept_reads_seg2.bam,2M/tmp/left_kept_reads_seg3.bam,2M/tmp/left_kept_reads_seg4.bam 2M/tmp/left_kept_reads_seg1.to_spliced.bam,2M/tmp/left_kept_reads_seg2.to_spliced.bam,2M/tmp/left_kept_reads_seg3.to_spliced.bam,2M/tmp/left_kept_reads_seg4.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 2M/ --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 -p8 --no-closure-search --no-coverage-search --no-microexon-search --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_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/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel.fa 2M/junctions.bed 2M/insertions.bed 2M/deletions.bed 2M/fusions.out 2M/tmp/accepted_hits 2M/tmp/left_kept_reads.mapped.bam,2M/tmp/left_kept_reads.candidates 2M/tmp/left_kept_reads.bam
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort 2M/tmp/accepted_hits0.bam 2M/tmp/accepted_hits0_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort 2M/tmp/accepted_hits1.bam 2M/tmp/accepted_hits1_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort 2M/tmp/accepted_hits2.bam 2M/tmp/accepted_hits2_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort 2M/tmp/accepted_hits3.bam 2M/tmp/accepted_hits3_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort 2M/tmp/accepted_hits4.bam 2M/tmp/accepted_hits4_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort 2M/tmp/accepted_hits5.bam 2M/tmp/accepted_hits5_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort 2M/tmp/accepted_hits6.bam 2M/tmp/accepted_hits6_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 sort 2M/tmp/accepted_hits7.bam 2M/tmp/accepted_hits7_sorted
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/samtools_0.1.18 merge -f -h 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam 2M/accepted_hits.bam 2M/tmp/accepted_hits0_sorted.bam 2M/tmp/accepted_hits1_sorted.bam 2M/tmp/accepted_hits2_sorted.bam 2M/tmp/accepted_hits3_sorted.bam 2M/tmp/accepted_hits4_sorted.bam 2M/tmp/accepted_hits5_sorted.bam 2M/tmp/accepted_hits6_sorted.bam 2M/tmp/accepted_hits7_sorted.bam
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/bam_merge -Q --sam-header 2M/tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam 2M/unmapped.bam 2M/tmp/unmapped_left_0.bam 2M/tmp/unmapped_left_1.bam 2M/tmp/unmapped_left_2.bam 2M/tmp/unmapped_left_3.bam 2M/tmp/unmapped_left_4.bam 2M/tmp/unmapped_left_5.bam 2M/tmp/unmapped_left_6.bam 2M/tmp/unmapped_left_7.bam
#>alldone: