/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat -r 236 -o /projects/NBL/HS1799/61074AAXX_4/tophat /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat/61074AAXX_4_1.fastq /projects/NBL/HS1799/61074AAXX_4/tophat/61074AAXX_4_2.fastq
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1799/61074AAXX_4/tophat/ --max-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 --inner-dist-mean 236 --inner-dist-std-dev 20 --no-microexon-search --fastq /projects/NBL/HS1799/61074AAXX_4/tophat/61074AAXX_4_1.fastq
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1799/61074AAXX_4/tophat/ --max-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 --inner-dist-mean 236 --inner-dist-std-dev 20 --no-microexon-search --fastq /projects/NBL/HS1799/61074AAXX_4/tophat/61074AAXX_4_2.fastq
bowtie -q --un /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileBc9jen
/home/rcorbett/aligners/tophat/tophat-1.0.13/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 /projects/NBL/HS1799/61074AAXX_4/tophat/ --max-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 --inner-dist-mean 236 --inner-dist-std-dev 20 --no-microexon-search /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq /dev/null /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads.bwtout  > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileWVdfeB
bowtie -q --un /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filewpseMQ
bowtie -q --un /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filedBuQFH
bowtie -q --un /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg3.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filer7ZXRr
bowtie -q --un /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileo1W8hL
/home/rcorbett/aligners/tophat/tophat-1.0.13/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 /projects/NBL/HS1799/61074AAXX_4/tophat/ --max-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 --inner-dist-mean 236 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq /dev/null /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads.bwtout  > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filezOvb5v
bowtie -q --un /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filehr7FPB
bowtie -q --un /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileHTzVJC
bowtie -q --un /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg3.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileYhrFJJ
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1799/61074AAXX_4/tophat/ --max-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 --inner-dist-mean 236 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --ium-reads /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg1_missing.fq,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg2_missing.fq,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg3_missing.fq,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg1_missing.fq,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg2_missing.fq,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg3_missing.fq /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//segment.juncs /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg2.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg3.bwtout /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg2.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg3.bwtout
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/juncs_db 3 25 /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//segment.juncs /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa
bowtie-build /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs.fa /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileR4YjC9
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filet5a5Wr
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/left_kept_reads_seg3.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileViFWmy
/home/rcorbett/aligners/tophat/tophat-1.0.13/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 /projects/NBL/HS1799/61074AAXX_4/tophat/ --max-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 --inner-dist-mean 236 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//segment.juncs /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg2.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg3.bwtout /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg2_to_spliced.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//left_kept_reads_seg3_to_spliced.bwtout > /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=/projects/NBL/HS1799/61074AAXX_4/tophat/tmp/ /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileWVdfeB /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq.candidate_hits.sam > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filer3CiaR
mv /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filer3CiaR /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq.candidate_hits.sam
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filerHx3xT
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileYwH2dn
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_4/tophat//tmp/right_kept_reads_seg3.fq - > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileghC6vS
/home/rcorbett/aligners/tophat/tophat-1.0.13/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 /projects/NBL/HS1799/61074AAXX_4/tophat/ --max-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 --inner-dist-mean 236 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//segment.juncs /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg2.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg3.bwtout /projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg2_to_spliced.bwtout,/projects/NBL/HS1799/61074AAXX_4/tophat/tmp//right_kept_reads_seg3_to_spliced.bwtout > /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=/projects/NBL/HS1799/61074AAXX_4/tophat/tmp/ /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filezOvb5v /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq.candidate_hits.sam > /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileD2ftir
mv /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/fileD2ftir /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq.candidate_hits.sam
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1799/61074AAXX_4/tophat/ --max-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 --inner-dist-mean 236 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search junctions.bed accepted_hits.sam /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq.candidate_hits.sam /projects/NBL/HS1799/61074AAXX_4/tophat/left_kept_reads.fq /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq.candidate_hits.sam /projects/NBL/HS1799/61074AAXX_4/tophat/right_kept_reads.fq
sort -k 3,3 -k 4,4n --temporary-directory=/projects/NBL/HS1799/61074AAXX_4/tophat/tmp/ /projects/NBL/HS1799/61074AAXX_4/tophat/accepted_hits.sam > <open file '/projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filelgeljO', mode 'a' at 0x2a963d2378>
mv <open file '/projects/NBL/HS1799/61074AAXX_4/tophat/tmp/filelgeljO', mode 'a' at 0x2a963d2378> /projects/NBL/HS1799/61074AAXX_4/tophat/accepted_hits.sam
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/wiggles /projects/NBL/HS1799/61074AAXX_4/tophat/accepted_hits.sam /projects/NBL/HS1799/61074AAXX_4/tophat/coverage.wig