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?
Solved. Seems it is a threading issue. When I have removed
-@8
from the code, there is no error or warning.
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.
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was ref_sequence.fa the very same fasta sequence fasta that was used to map the reads from sample.bam ?
Yes. I am suspecting is it a multithreading issue?
That seems unlikely.