Using tophat v1.1.4, I have run into some issues with running tophat on the Illumina Human Body Map data. Here is some information from the log files from the run.
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Last few lines of output from the tophat run:
[Sat Jan 8 02:13:21 2011] Mapping reads against segment_juncs with Bowtie
[Sat Jan 8 02:16:29 2011] Joining segment hits
[Sat Jan 8 02:22:00 2011] Reporting output tracks
Error: could not convert to BAM with samtools
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Last line from run.log:
samtools view -S -b ./trim_to_75_trim_s_8_sequence_end1_tophat_out//tmp/accepted_hits.sam > ./trim_to_75_trim_s_8_sequence_end1_tophat_out//tmp/file9j1TKZ
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Error message From accepted_hits_sam_to_bam.log:
[samopen] SAM header is present: 25 sequences.
Parse error at line 1129818: CIGAR and sequence length are inconsistent
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Any idea what is going on and/or how I should go about solving it?
Edit:
Another thing I want to point out is that I saw that there was an accepted_hits.sam file in the tmp folder that remained after the tophat runs failed to complete. I tried to run this in Cufflinks instead and was getting errors that the sam file was not ordered correctly. I am posting this information in case that can help with understanding what might be happening with this issue.
---
Last few lines of output from the tophat run:
[Sat Jan 8 02:13:21 2011] Mapping reads against segment_juncs with Bowtie
[Sat Jan 8 02:16:29 2011] Joining segment hits
[Sat Jan 8 02:22:00 2011] Reporting output tracks
Error: could not convert to BAM with samtools
---
---
Last line from run.log:
samtools view -S -b ./trim_to_75_trim_s_8_sequence_end1_tophat_out//tmp/accepted_hits.sam > ./trim_to_75_trim_s_8_sequence_end1_tophat_out//tmp/file9j1TKZ
---
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Error message From accepted_hits_sam_to_bam.log:
[samopen] SAM header is present: 25 sequences.
Parse error at line 1129818: CIGAR and sequence length are inconsistent
---
Any idea what is going on and/or how I should go about solving it?
Edit:
Another thing I want to point out is that I saw that there was an accepted_hits.sam file in the tmp folder that remained after the tophat runs failed to complete. I tried to run this in Cufflinks instead and was getting errors that the sam file was not ordered correctly. I am posting this information in case that can help with understanding what might be happening with this issue.
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