/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat -r 236 -o /projects/NBL/HS1799/61074AAXX_3/tophat /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1799/61074AAXX_3/tophat/61074AAXX_3_1.fastq /projects/NBL/HS1799/61074AAXX_3/tophat/61074AAXX_3_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_3/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_3/tophat/61074AAXX_3_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_3/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_3/tophat/61074AAXX_3_2.fastq
bowtie -q --un /projects/NBL/HS1799/61074AAXX_3/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_3/tophat/left_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat/left_kept_reads.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileYIcMfL
/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_3/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_3/tophat/left_kept_reads.fq /dev/null /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads.bwtout  > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/filenF8dl3
bowtie -q --un /projects/NBL/HS1799/61074AAXX_3/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_3/tophat//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileZkNEy4
bowtie -q --un /projects/NBL/HS1799/61074AAXX_3/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_3/tophat//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileJTKPAM
bowtie -q --un /projects/NBL/HS1799/61074AAXX_3/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_3/tophat//tmp/left_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg3.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileWzGyKj
bowtie -q --un /projects/NBL/HS1799/61074AAXX_3/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_3/tophat/right_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat/right_kept_reads.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/filem9u0cq
/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_3/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_3/tophat/right_kept_reads.fq /dev/null /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads.bwtout  > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileF8mHDw
bowtie -q --un /projects/NBL/HS1799/61074AAXX_3/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_3/tophat//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileEHANw0
bowtie -q --un /projects/NBL/HS1799/61074AAXX_3/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_3/tophat//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileRtpU34
bowtie -q --un /projects/NBL/HS1799/61074AAXX_3/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_3/tophat//tmp/right_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg3.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileGdOXBL
/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_3/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_3/tophat/tmp//left_kept_reads_seg1_missing.fq,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg2_missing.fq,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg3_missing.fq,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg1_missing.fq,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg2_missing.fq,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg3_missing.fq /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//segment.juncs /projects/NBL/HS1799/61074AAXX_3/tophat/left_kept_reads.fq /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg2.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg3.bwtout /projects/NBL/HS1799/61074AAXX_3/tophat/right_kept_reads.fq /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg2.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg3.bwtout
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/juncs_db 3 25 /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//segment.juncs /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa
bowtie-build /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs.fa /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileRW18o2
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileL5Pzl0
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/left_kept_reads_seg3.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/filed7CSzi
/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_3/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_3/tophat/left_kept_reads.fq /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//segment.juncs /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg2.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg3.bwtout /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg2_to_spliced.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//left_kept_reads_seg3_to_spliced.bwtout > /projects/NBL/HS1799/61074AAXX_3/tophat/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=/projects/NBL/HS1799/61074AAXX_3/tophat/tmp/ /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/filenF8dl3 /projects/NBL/HS1799/61074AAXX_3/tophat/left_kept_reads.fq.candidate_hits.sam > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileVg0XBP
mv /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileVg0XBP /projects/NBL/HS1799/61074AAXX_3/tophat/left_kept_reads.fq.candidate_hits.sam
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileiEo1zW
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileW6djrf
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1799/61074AAXX_3/tophat//tmp/right_kept_reads_seg3.fq - > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileomNl7B
/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_3/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_3/tophat/right_kept_reads.fq /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//segment.juncs /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg2.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg3.bwtout /projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg2_to_spliced.bwtout,/projects/NBL/HS1799/61074AAXX_3/tophat/tmp//right_kept_reads_seg3_to_spliced.bwtout > /projects/NBL/HS1799/61074AAXX_3/tophat/right_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=/projects/NBL/HS1799/61074AAXX_3/tophat/tmp/ /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileF8mHDw /projects/NBL/HS1799/61074AAXX_3/tophat/right_kept_reads.fq.candidate_hits.sam > /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileLx95A9
mv /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileLx95A9 /projects/NBL/HS1799/61074AAXX_3/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_3/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_3/tophat/left_kept_reads.fq.candidate_hits.sam /projects/NBL/HS1799/61074AAXX_3/tophat/left_kept_reads.fq /projects/NBL/HS1799/61074AAXX_3/tophat/right_kept_reads.fq.candidate_hits.sam /projects/NBL/HS1799/61074AAXX_3/tophat/right_kept_reads.fq
sort -k 3,3 -k 4,4n --temporary-directory=/projects/NBL/HS1799/61074AAXX_3/tophat/tmp/ /projects/NBL/HS1799/61074AAXX_3/tophat/accepted_hits.sam > <open file '/projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileZUOfQH', mode 'a' at 0x2a963d2378>
mv <open file '/projects/NBL/HS1799/61074AAXX_3/tophat/tmp/fileZUOfQH', mode 'a' at 0x2a963d2378> /projects/NBL/HS1799/61074AAXX_3/tophat/accepted_hits.sam
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/wiggles /projects/NBL/HS1799/61074AAXX_3/tophat/accepted_hits.sam /projects/NBL/HS1799/61074AAXX_3/tophat/coverage.wig