/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat -r 241 -o /projects/NBL/HS1795/700FNAAXX_8/tophat_wj -G /projects/NBL/reference_files/UCSC/all.gtf.gff3 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/700FNAAXX_8_1_export.txt.fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/700FNAAXX_8_2_export.txt.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/HS1795/700FNAAXX_8/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 241 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/700FNAAXX_8_1_export.txt.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/HS1795/700FNAAXX_8/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 241 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/700FNAAXX_8_2_export.txt.fastq
bowtie -q --un /projects/NBL/HS1795/700FNAAXX_8/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/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filejBpNFE
/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/HS1795/700FNAAXX_8/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 241 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq /dev/null /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads.bwtout  > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filercgi94
bowtie -q --un /projects/NBL/HS1795/700FNAAXX_8/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/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filelqO0If
bowtie -q --un /projects/NBL/HS1795/700FNAAXX_8/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/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/file9CD6Sb
bowtie -q --un /projects/NBL/HS1795/700FNAAXX_8/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/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg3.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filetAO7mJ
bowtie -q --un /projects/NBL/HS1795/700FNAAXX_8/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/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/fileb4T9OE
/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/HS1795/700FNAAXX_8/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 241 --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/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq /dev/null /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads.bwtout  > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/fileH9TvC6
bowtie -q --un /projects/NBL/HS1795/700FNAAXX_8/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/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/fileDkw1zs
bowtie -q --un /projects/NBL/HS1795/700FNAAXX_8/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/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/file59OowZ
bowtie -q --un /projects/NBL/HS1795/700FNAAXX_8/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/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg3.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/file9CORWg
/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/HS1795/700FNAAXX_8/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 241 --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/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg1_missing.fq,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg2_missing.fq,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg3_missing.fq,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg1_missing.fq,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg2_missing.fq,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg3_missing.fq /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//segment.juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg2.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg3.bwtout /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg2.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg3.bwtout
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/juncs_db 3 25 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/all.juncs,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//segment.juncs /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa
bowtie-build /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/segment_juncs.fa /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/segment_juncs
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/segment_juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filepcUMxy
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/segment_juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/fileXqQdmZ
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/segment_juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/left_kept_reads_seg3.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filePJRoLH
/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/HS1795/700FNAAXX_8/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 241 --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/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/all.juncs,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//segment.juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg2.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg3.bwtout /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg2_to_spliced.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//left_kept_reads_seg3_to_spliced.bwtout > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/ /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filercgi94 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq.candidate_hits.sam > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filef8OHSL
mv /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filef8OHSL /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq.candidate_hits.sam
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/segment_juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filebByqmx
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/segment_juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filePAJ1ok
bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/segment_juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg3.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj//tmp/right_kept_reads_seg3.fq - > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filepgLiqA
/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/HS1795/700FNAAXX_8/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 241 --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/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/all.juncs,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//segment.juncs /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg2.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg3.bwtout /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg2_to_spliced.bwtout,/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp//right_kept_reads_seg3_to_spliced.bwtout > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/ /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/fileH9TvC6 /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq.candidate_hits.sam > /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filejwaGCp
mv /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filejwaGCp /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/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/HS1795/700FNAAXX_8/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 241 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-coverage-search --no-microexon-search junctions.bed accepted_hits.sam /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq.candidate_hits.sam /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/left_kept_reads.fq /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq.candidate_hits.sam /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/right_kept_reads.fq
sort -k 3,3 -k 4,4n --temporary-directory=/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/ /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/accepted_hits.sam > <open file '/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filezbXVH3', mode 'a' at 0x2a98a306c0>
mv <open file '/projects/NBL/HS1795/700FNAAXX_8/tophat_wj/tmp/filezbXVH3', mode 'a' at 0x2a98a306c0> /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/accepted_hits.sam
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/wiggles /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/accepted_hits.sam /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/coverage.wig