cram to bam conversion
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4.7 years ago
irfanwustl ▴ 80

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 • 5.2k views
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0
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was ref_sequence.fa the very same fasta sequence fasta that was used to map the reads from sample.bam ?

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Yes. I am suspecting is it a multithreading issue?

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That seems unlikely.

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4.7 years ago
irfanwustl ▴ 80

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

-@8

from the code, there is no error or warning.

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

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