With tophat 2.0.3, I get a segfault from tophat reports
[...clipped output for clarity...]
[2012-06-02 18:19:12] Mapping left_kept_reads_seg28 to genome segment_juncs with Bowtie2 (28/28)
[2012-06-02 18:19:13] Joining segment hits
[2012-06-02 18:21:29] Reporting output tracks
[FAILED]
Error running /u2/home/miseiler/Desktop/tophat-2.0.3.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 bowtie2_unaligned_100/ --max-multihits 20 --max-seg-multihits 40 --segment-length 100 --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 --max-mismatches 2 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p8 --no-closure-search --no-coverage-search --no-microexon-search --sam-header bowtie2_unaligned_100/tmp/hg19_genome.bwt.samheader.sam --samtools=/home/miseiler/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /home/miseiler/Projects/mssm/data/seq/hg19.fa bowtie2_unaligned_100/junctions.bed bowtie2_unaligned_100/insertions.bed bowtie2_unaligned_100/deletions.bed bowtie2_unaligned_100/fusions.out bowtie2_unaligned_100/tmp/accepted_hits bowtie2_unaligned_100/tmp/left_kept_reads.candidates_and_unspl.bam bowtie2_unaligned_100/tmp/left_kept_reads.bam
Loading ...done
Running that command by itself gives the following:
tophat_reports v2.0.3 (3443S)
---------------------------------------
[samopen] SAM header is present: 25 sequences.
Loading chr1...done
[...more chromosomes...]
Loading chrM...done
Loading ...done
zsh: segmentation fault (core dumped) /u2/home/miseiler/Desktop/tophat-2.0.3.Linux_x86_64/tophat_reports 8 0 50
Unfortunately, I have tried running earlier tophat_report versions from the tophat2 series and they simply segfault without even opening hg19.fa.
Anyone seeing this?
[...clipped output for clarity...]
[2012-06-02 18:19:12] Mapping left_kept_reads_seg28 to genome segment_juncs with Bowtie2 (28/28)
[2012-06-02 18:19:13] Joining segment hits
[2012-06-02 18:21:29] Reporting output tracks
[FAILED]
Error running /u2/home/miseiler/Desktop/tophat-2.0.3.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 bowtie2_unaligned_100/ --max-multihits 20 --max-seg-multihits 40 --segment-length 100 --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 --max-mismatches 2 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p8 --no-closure-search --no-coverage-search --no-microexon-search --sam-header bowtie2_unaligned_100/tmp/hg19_genome.bwt.samheader.sam --samtools=/home/miseiler/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /home/miseiler/Projects/mssm/data/seq/hg19.fa bowtie2_unaligned_100/junctions.bed bowtie2_unaligned_100/insertions.bed bowtie2_unaligned_100/deletions.bed bowtie2_unaligned_100/fusions.out bowtie2_unaligned_100/tmp/accepted_hits bowtie2_unaligned_100/tmp/left_kept_reads.candidates_and_unspl.bam bowtie2_unaligned_100/tmp/left_kept_reads.bam
Loading ...done
Running that command by itself gives the following:
tophat_reports v2.0.3 (3443S)
---------------------------------------
[samopen] SAM header is present: 25 sequences.
Loading chr1...done
[...more chromosomes...]
Loading chrM...done
Loading ...done
zsh: segmentation fault (core dumped) /u2/home/miseiler/Desktop/tophat-2.0.3.Linux_x86_64/tophat_reports 8 0 50
Unfortunately, I have tried running earlier tophat_report versions from the tophat2 series and they simply segfault without even opening hg19.fa.
Anyone seeing this?
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