I'm using bowtie1 to align reads from a big dataset (100gb Illumina reads vs 5gb Pacbio reads) and I have created a pipeline to split the alignment in smaller chunks and I'm running the command on an HPC.
I have the output files and it seems that the alignment worked for all 100 chunks.
However in a few cases when I checked the log.file I found this error:
Time loading forward index: 00:00:00 Error outputting data terminate called after throwing an instance of 'int'
The HPC error file is also reporting an error:
line 26: 30288 Aborted bowtie -a -t -5 0 -3 5 -p 32 -v 0 ........
Despite these errors, bowtie is generating the output files and they seem to be correct.
Any suggestions?
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Is "ungapped" alignments the reason you are using
bowtie v.1.xin this case? Have you checked the index (which I assume is made from PacBio reads) usingbowtie-inspect?Thanks for the reply,
Yes my alignment must be ungapped. I checked the index and is fine also because the error is not related to any particular indexed chunks but happens randomly at every new run.
It might be that i have just to play around with memory usage with my HPC.
This is the command-line that i'm using:
During the indexing and the alignments, the files are moved one by one in a temporary directory and then copied in a final directory.
Let me know what do you think.
Best