Jing -
No experience with exactly this behavior or with no output
generated. Our experience, however, is that samtools seems
not to check for EOF on its input. Instead, it stops whenever
the next disk read returns nothing. Thus, when reading from
a networked file system it sometimes stops early, without
giving any indication that it has done so.
We routinely check the coverage for some reference contig near
the end of the reference sequence .fasta file. (The very last
contig in the build 38 reference is HLA and it doesn't always
have anything mapped to it.)
At a guess, this might be what occurred for you. Unlikely that
the available memory has anything to do with it. I would try
the bad example several times and see whether there is any
variation in the behavior.
- tom blackwell -
On Tue, 2 Jan 2018, Hu Jing wrote:
Thank you, Adrian. Happy New Year!
Highly appreciate if anyone could help answer my questions regarding the
samtools error when converting SAM to BAM or at least give some hints or clues.
Thanks so much!
Jing
On Dec 25, 2017, at 6:22 PM, Adrian Pelin
<apeli...@gmail.com<mailto:apeli...@gmail.com>> wrote:
Merry Christmas!
On Mon, Dec 25, 2017 at 7:57 PM Hu Jing
<hj_hanna2...@hotmail.com<mailto:hj_hanna2...@hotmail.com>> wrote:
To whom it may concern,
Recently we ran into an issue with converting SAM to BAM using samtools view
command called in python, please see the commands below,
cmd = 'samtools view -b -o {} {}'.format(output_BAM, input_SAM)
os.system(cmd)
The SAM was generated from the Bowtie2, and appended with a few more tags
defined by our own, such as sequence of UMI (unique molecular index). The SAM
file is ~4Gb in size. The samtools we're using is version 1.3.1.
When we tried to run the above command in a VM with 32Gb RAM, it failed
silently, and we couldn't see the BAM file generated. After we increased to
64Gb RAM, the BAM was generated.
Wonder why increasing the RAM could help the conversion of SAM to BAM (64Gb is
really big compared to the SAM size 4Gb)? Is there any option that we may use
to print the logs for easier troubleshooting?
Thanks so much and happy holidays!
Jing
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