Tophat: some .sam files empty and some not

[oliviera]

Dear All,

I am running tophat on 7 datasets of 76bp paired end reads.
In one case the accepted_hits.sam file is empty while the 6 others are looking good. The fastq file this particular experiment is ok and the Eland mapping is looking good as well (at least 70% of mapped read). I have run it again and it gave the same thing....

Below is part of the run.log file from tophat (do not know if this help to understand what is going on).
I found this thread which describe something similar but in my case I do get nice results from the other runs...

http://seqanswers.com/forums/showthread.php?t=2707

Any idea??

olivier

bowtie -q -v 2 -p 4 -k 40 -m 40 /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/segment_juncs /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel//tmp/right_kept_reads_seg3.fq | /bin/bin/fix_map_ordering --fastq /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel//tmp/right_kept_reads_seg3.fq - > /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/filex5PUBO
/bin/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 /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/ --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 50 --inner-dist-std-dev 20 --gff-annotations /home/olivier/src/bowtie-0.12.5/genomes/Danio_rerio.Zv8.57.out.gff --no-closure-search --no-coverage-search --no-microexon-search /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/right_kept_reads.fq /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/Danio_rerio.juncs,/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp//segment.juncs /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp//right_kept_reads_seg1.bwtout,/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp//right_kept_reads_seg2.bwtout,/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp//right_kept_reads_seg3.bwtout /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp//right_kept_reads_seg1_to_spliced.bwtout,/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp//right_kept_reads_seg2_to_spliced.bwtout,/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp//right_kept_reads_seg3_to_spliced.bwtout > /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/right_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/ /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/fileNXjJUj /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/right_kept_reads.fq.candidate_hits.sam > /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/fileTwcDqL
mv /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/fileTwcDqL /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/right_kept_reads.fq.candidate_hits.sam
/bin/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/ --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 50 --inner-dist-std-dev 20 --gff-annotations /home/olivier/src/bowtie-0.12.5/genomes/Danio_rerio.Zv8.57.out.gff --no-closure-search --no-coverage-search --no-microexon-search junctions.bed accepted_hits.sam /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/left_kept_reads.fq.candidate_hits.sam /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/left_kept_reads.fq /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/right_kept_reads.fq.candidate_hits.sam /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/right_kept_reads.fq
sort -k 3,3 -k 4,4n --temporary-directory=/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/ /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/accepted_hits.sam > <open file '/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/fileFfpBLA', mode 'a' at 0x7f67e3d503f0>
mv <open file '/home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/tmp/fileFfpBLA', mode 'a' at 0x7f67e3d503f0> /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/accepted_hits.sam
/bin/bin/wiggles /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/accepted_hits.sam /home/olivier/Olivier_data_ITG/Solexa_24hpf_july2010/s_2_results_gffinput_withnovel/coverage.wig