Dear all:
My tophat was updated from 1.3.1 to 1.3.3 last week and
I've met a weird problem recently.
If I run the command like "tophat -p 8 --keep-tmp /my/bowtie_ref/path/refname /my/seq/path/sequence.fq", I'll get the following error msgs:
Error executing: /opt/ngs_tools/tophat-1.3.3/bin/bam_merge ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam ./tophat_out/tmp/left_kept_reads.unspl.bam ./tophat_out/tmp/left_kept_reads.candidates.bam
Owing to the temp files were kept, I check wether the files, "left_kept_reads.unspl.bam", and "left_kept_reads.candidates.bam" is in ./tophat_out/tmp/ folder or not. These two files did exist.
However, I ran the command "/opt/ngs_tools/tophat-1.3.3/bin/bam_merge ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam ./tophat_out/tmp/left_kept_reads.unspl.bam ./tophat_out/tmp/left_kept_reads.candidates.bam" again, I got the following error msgs:
Warning: no input BAM records found.
GList error (GList.hh:932):Invalid list index: 0
I don't know why there is no input BAM records. SO WIERED!!!
Are there anyone can help me? Thanks a lot
Best,
Yi
My tophat was updated from 1.3.1 to 1.3.3 last week and
I've met a weird problem recently.
If I run the command like "tophat -p 8 --keep-tmp /my/bowtie_ref/path/refname /my/seq/path/sequence.fq", I'll get the following error msgs:
Error executing: /opt/ngs_tools/tophat-1.3.3/bin/bam_merge ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam ./tophat_out/tmp/left_kept_reads.unspl.bam ./tophat_out/tmp/left_kept_reads.candidates.bam
Owing to the temp files were kept, I check wether the files, "left_kept_reads.unspl.bam", and "left_kept_reads.candidates.bam" is in ./tophat_out/tmp/ folder or not. These two files did exist.
However, I ran the command "/opt/ngs_tools/tophat-1.3.3/bin/bam_merge ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam ./tophat_out/tmp/left_kept_reads.unspl.bam ./tophat_out/tmp/left_kept_reads.candidates.bam" again, I got the following error msgs:
Warning: no input BAM records found.
GList error (GList.hh:932):Invalid list index: 0
I don't know why there is no input BAM records. SO WIERED!!!
Are there anyone can help me? Thanks a lot
Best,
Yi
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