/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat -r 245 -o /projects/NBL/HS1803/616GYAAXX_6/tophat_wj -G /projects/NBL/reference_files/UCSC/all.gtf.gff3 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_1.fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_2.fastq
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/gff_juncs /projects/NBL/reference_files/UCSC/all.gtf.gff3
/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/HS1803/616GYAAXX_6/tophat_wj/ --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 245 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_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/HS1803/616GYAAXX_6/tophat_wj/ --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 245 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_2.fastq
bowtie -q --un /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/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/HS1803/616GYAAXX_6/tophat_wj/left_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/left_kept_reads.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/fileoIMAPI
/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/HS1803/616GYAAXX_6/tophat_wj/ --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 245 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/left_kept_reads.fq /dev/null /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads.bwtout  > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/file7MueWf
bowtie -q --un /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/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/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/fileqCTn3x
bowtie -q --un /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/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/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/fileToo97M
bowtie -q --un /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/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/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg3.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/filemDLHLo
bowtie -q --un /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/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/HS1803/616GYAAXX_6/tophat_wj/right_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/right_kept_reads.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/filelUHdTI
/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/HS1803/616GYAAXX_6/tophat_wj/ --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 245 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-coverage-search --no-microexon-search /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/right_kept_reads.fq /dev/null /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//right_kept_reads.bwtout  > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/fileGaYCZt
bowtie -q --un /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/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/HS1803/616GYAAXX_6/tophat_wj//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/filejmBOqw
bowtie -q --un /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/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/HS1803/616GYAAXX_6/tophat_wj//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/filecw3Zaf
bowtie -q --un /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/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/HS1803/616GYAAXX_6/tophat_wj//tmp/right_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/right_kept_reads_seg3.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/filerNbsXy
/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/HS1803/616GYAAXX_6/tophat_wj/ --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 245 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-coverage-search --no-microexon-search --ium-reads /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg1_missing.fq,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg2_missing.fq,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg3_missing.fq,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//right_kept_reads_seg1_missing.fq,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//right_kept_reads_seg2_missing.fq,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//right_kept_reads_seg3_missing.fq /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//segment.juncs /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/left_kept_reads.fq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg2.bwtout,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg3.bwtout /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/right_kept_reads.fq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//right_kept_reads_seg2.bwtout,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//right_kept_reads_seg3.bwtout
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/juncs_db 3 25 /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/all.juncs,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//segment.juncs /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa
bowtie-build /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs.fa /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/file8mKYMU
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/filePCkULE
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj//tmp/left_kept_reads_seg3.fq - > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/fileUsdBBp
/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/HS1803/616GYAAXX_6/tophat_wj/ --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 245 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-coverage-search --no-microexon-search /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/left_kept_reads.fq /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/all.juncs,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//segment.juncs /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg2.bwtout,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg3.bwtout /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg2_to_spliced.bwtout,/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp//left_kept_reads_seg3_to_spliced.bwtout > /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/left_kept_reads.fq.candidate_hits.sam