One issue with exome data could be that it has very reads which map to the
Mt genome.
Could you turn of the tmp file deletion parameter, and then check if the
tmp_23742.bam file has any reads mapped or not.
If not, then check if the corresponding Sam file tmp423742.sam has mapped
reads.
If the Sam file is also devoid of reads, that might indicate a Hisar
alingment issue.
If the sam and the bam filea have reads, then probably the sample did not
have much mitochondrial reads, thus the extraction of unmapped and
mitochondrial reads did not finish cleanly.
Hello,
I run MitoSalt on paired end fastq.gz files of exome but got Killed after
Extract reads:
~~~
Thu Sep 30 10:44:03 2021: Map to NU+MT genome
Thu Sep 30 10:53:49 2021: Extract reads
Killed [E::hts_open_format] Failed to open file tmp_23742.bam
~~~
Is that posible to run MitoSalt on exome raw data? Should I change some
parameters on the script commands?
Hello,
I run MitoSalt on paired end fastq.gz files of exome but got Killed after Extract reads:
Is that posible to run MitoSalt on exome raw data? Should I change some parameters on the script commands?
The log file is attached.
Thank you in advance,
Adily
Last edit: adily basal 2021-09-30
Hi Adily,
One issue with exome data could be that it has very reads which map to the
Mt genome.
Could you turn of the tmp file deletion parameter, and then check if the
tmp_23742.bam file has any reads mapped or not.
If not, then check if the corresponding Sam file tmp423742.sam has mapped
reads.
If the Sam file is also devoid of reads, that might indicate a Hisar
alingment issue.
If the sam and the bam filea have reads, then probably the sample did not
have much mitochondrial reads, thus the extraction of unmapped and
mitochondrial reads did not finish cleanly.
Could you try this and let us know.
Thanks and regards
Swaraj
On Thu, Sep 30, 2021, 4:00 PM adily basal adily@users.sourceforge.net
wrote: