cram to bam conversion

Question

[irfanwustl]

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?

[Pierre Lindenbaum]

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

[irfanwustl]

Yes. I am suspecting is it a multithreading issue?

[WouterDeCoster]

That seems unlikely.

Answer 1

[irfanwustl]

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

-@8

from the code, there is no error or warning.

[finswimmer]

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.

[h.mon]

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