Question: cram to bam conversion
0
gravatar for irfanwustl
10 months ago by
irfanwustl0
irfanwustl0 wrote:

I am trying to convert cram file to bam file but I am getting the following error:

[E::cram_get_ref] Failed to populate reference for id 504

[E::cram_get_ref] Failed to populate reference for id 538

[E::cram_get_ref] Failed to populate reference for id 608

.........................................................................................

The code I am using:

samtools view -b -T ref_sequence.fa -o $sample.bam -@8 $sample.cram

Any idea?

alignment genome • 561 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by irfanwustl0

was ref_sequence.fa the very same fasta sequence fasta that was used to map the reads from sample.bam ?

ADD REPLYlink modified 10 months ago • written 10 months ago by Pierre Lindenbaum129k

Yes. I am suspecting is it a multithreading issue?

ADD REPLYlink written 10 months ago by irfanwustl0

That seems unlikely.

ADD REPLYlink written 10 months ago by WouterDeCoster44k
0
gravatar for irfanwustl
10 months ago by
irfanwustl0
irfanwustl0 wrote:

Solved. Seems it is a threading issue. When I have removed

-@8

from the code, there is no error or warning.

ADD COMMENTlink written 10 months ago by irfanwustl0

What version of samtools do you use?

As WouterDeCoster said, this seems unlikely to be the reason for me as well. If it is, than it's a bug and you should report it at samtools issue tracker.

ADD REPLYlink written 10 months ago by finswimmer13k

If instead of -@ you use --threads, do you have the same error?

ADD REPLYlink written 10 months ago by h.mon30k
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