Dear all,
while running Tophat2 (default parameters, 64 bit centos), we keep encountering the following warning towards the end of the run:
We tried with Tophat v 2.0.4 and Tophat 2.0.5, paired with Bowtie v2beta7 and Samtools 0.1.18
My first guess was "lack of disk space", but we tried with terabytes of space, and the thing is still happening (in a deterministic way, the warnings are identical by number of "[main_samview] truncated file" lines).
The problem is not directly translated into a read loss. The number of read pairs contained in the sum accepted_hits.bam and unmapped.bam is always the same as the input fastq files. Any clue? Should we worry? Has anyone found the same problem?
Federico
while running Tophat2 (default parameters, 64 bit centos), we keep encountering the following warning towards the end of the run:
Code:
Warning: couldn't remove all temporary files in /path ----------------------------------------------- [2012-10-17 18:32:54] Run complete: 01:26:19 elapsed [main_samview] truncated file. [main_samview] truncated file. [main_samview] truncated file.
My first guess was "lack of disk space", but we tried with terabytes of space, and the thing is still happening (in a deterministic way, the warnings are identical by number of "[main_samview] truncated file" lines).
The problem is not directly translated into a read loss. The number of read pairs contained in the sum accepted_hits.bam and unmapped.bam is always the same as the input fastq files. Any clue? Should we worry? Has anyone found the same problem?
Federico
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