Question

cram to bam conversion

1

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4.5 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 • 5.0k views

ADD COMMENT • link 4.5 years ago by irfanwustl ▴ 80

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

ADD REPLY • link 4.5 years ago by Pierre Lindenbaum 161k

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Yes. I am suspecting is it a multithreading issue?

ADD REPLY • link 4.5 years ago by irfanwustl ▴ 80

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That seems unlikely.

ADD REPLY • link 4.5 years ago by WouterDeCoster 47k

score 2 · Accepted Answer · 2019-09-30

2

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4.5 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.

ADD COMMENT • link 4.5 years ago by irfanwustl ▴ 80

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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.

ADD REPLY • link 4.5 years ago by finswimmer 16k

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

ADD REPLY • link 4.5 years ago by h.mon 35k