/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./Mt_0_R1.TOnovel ../novelgene.v2 ./Mt_0_R1.TOnovel/R38_L5_Mt_0_sdlg_R1_nss_barcode_ACG.unmap_1.flt_1.fq
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_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 ./Mt_0_R1.TOnovel/ --max-multihits 10 --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 --sam-header ./Mt_0_R1.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq ./Mt_0_R1.TOnovel/R38_L5_Mt_0_sdlg_R1_nss_barcode_ACG.unmap_1.flt_1.fq
bowtie -q --un ./Mt_0_R1.TOnovel/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq - > ./Mt_0_R1.TOnovel/tmp/fileM4tFD9
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_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 ./Mt_0_R1.TOnovel/ --max-multihits 10 --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 --sam-header ./Mt_0_R1.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 ../novelgene.v2.fa ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./Mt_0_R1.TOnovel/tmp/left_kept_reads.bwtout  > ./Mt_0_R1.TOnovel/tmp/fileu3jqW1
bowtie -q --un ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1.fq - > ./Mt_0_R1.TOnovel/tmp/fileTIXKcf
bowtie -q --un ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2.fq - > ./Mt_0_R1.TOnovel/tmp/fileyeYpbx
bowtie -q --un ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3.fq - > ./Mt_0_R1.TOnovel/tmp/filebQvV2T
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_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 ./Mt_0_R1.TOnovel/ --max-multihits 10 --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 --sam-header ./Mt_0_R1.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search --ium-reads ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq,./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq,./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq ../novelgene.v2.fa ./Mt_0_R1.TOnovel/tmp/segment.juncs ./Mt_0_R1.TOnovel/tmp/segment.insertions ./Mt_0_R1.TOnovel/tmp/segment.deletions ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq ./Mt_0_R1.TOnovel/tmp/left_kept_reads.bwtout ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1.bwtout,./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2.bwtout,./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 ./Mt_0_R1.TOnovel/tmp/segment.juncs /dev/null /dev/null ../novelgene.v2.fa
bowtie-build ./Mt_0_R1.TOnovel/tmp/segment_juncs.fa ./Mt_0_R1.TOnovel/tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Mt_0_R1.TOnovel/tmp/segment_juncs ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1.fq - > ./Mt_0_R1.TOnovel/tmp/filedynXFR
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Mt_0_R1.TOnovel/tmp/segment_juncs ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2.fq - > ./Mt_0_R1.TOnovel/tmp/fileOQab0R
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Mt_0_R1.TOnovel/tmp/segment_juncs ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3.fq - > ./Mt_0_R1.TOnovel/tmp/fileSMvnUU
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_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 ./Mt_0_R1.TOnovel/ --max-multihits 10 --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 --sam-header ./Mt_0_R1.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search ../novelgene.v2.fa ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq ./Mt_0_R1.TOnovel/tmp/segment.juncs /dev/null /dev/null ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1.bwtout,./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2.bwtout,./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3.bwtout ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1_to_spliced.bwtout,./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2_to_spliced.bwtout,./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3_to_spliced.bwtout > ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./Mt_0_R1.TOnovel/tmp/ ./Mt_0_R1.TOnovel/tmp/fileu3jqW1 ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam > ./Mt_0_R1.TOnovel/tmp/fileHvRAQ2
sort -k 1,1n --temporary-directory=./Mt_0_R1.TOnovel/tmp/ ./Mt_0_R1.TOnovel/tmp/fileu3jqW1 ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./Mt_0_R1.TOnovel/tmp/fileHvRAQ2 ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_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 ./Mt_0_R1.TOnovel/ --max-multihits 10 --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 --sam-header ./Mt_0_R1.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search ./Mt_0_R1.TOnovel/junctions.bed ./Mt_0_R1.TOnovel/insertions.bed ./Mt_0_R1.TOnovel/deletions.bed ./Mt_0_R1.TOnovel/tmp/accepted_hits.sam ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam ./Mt_0_R1.TOnovel/tmp/left_kept_reads.fq
samtools view -S -b ./Mt_0_R1.TOnovel/tmp/accepted_hits.sam > ./Mt_0_R1.TOnovel/tmp/file2tDtvd
samtools sort ./Mt_0_R1.TOnovel/tmp/file2tDtvd ./Mt_0_R1.TOnovel/accepted_hits