Getting samtools cram-to-bam error “[E::cram_get_ref] Failed to populate reference for id”?

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#662 opened on Feb 23, 2018 1 comment 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 4/5
Estimated time: 3-5 days
Newbie friendliness: 30/100

Issue type: Bug
Clarity: Needs clarification
Activity status: Stale
Tech stack: c
Domain: bioinformatics

Research direction

Start with the samtools view command and the referenced file.cram, reference.fa, reference.dict, and log.txt. Trace the reported cram_get_ref failures and determine whether the conversion is expected to emit these errors; done means the cause and expected behavior are established.

Written by the indexing model from the issue text.

Description

I am trying to convert a cram to a bam using the following samtools command set-up:

samtools view -h -b -@ 16 file.cram -o file.bam -T reference.fa 2>&1 | tee -a log.txt

However, when I try this, I get the following error:

    [E::cram_get_ref] Failed to populate reference for id 76
    [E::cram_get_ref] Failed to populate reference for id 102
    [E::cram_get_ref] Failed to populate reference for id 129
    .
    .
    .
    .
    [continues for over 20 lines like this]

I'm not sure why I am getting this error. I've made sure to use the same reference file that was used to generate the cram (I was using a different reference file before) and have also included the reference.dict file.

It's also noteworthy that, although I'm getting this error, the cram file still gets converted to a bam and downstream processes like GATK are still able to run on the bam. It's just concerning to be getting such an error message.

Dominant language: C
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