BamUtil: recab error: failed to open reference genome

[statgen]

BamUtil: recab error: failed to open reference genome

[jonathonl]

Which version of bamUtil are you using? Can you try the NonPrimaryDedup branch.

[cbostwick87]

Hi Jonathon,
Thank you for your help! I cloned bamUtil (along with the other tools I am using) from the https://github.com/statgen/topmed_variant_calling Github repo. Therefore, I believe the version is v.1.0.15
When I click on the NonPrimaryDedup branch you linked (https://github.com/statgen/bamUtil/tree/NonPrimaryDedup), it also says it is version v.1.0.15, but I will try to clone it and use this bamUtil branch and report back.

After cloning and making the NonPrimaryDedup branch bamUtil, I tried to use the dedup --recab command as above, but it returned exactly the same errors (trying both reference genomes) as before.

[jonathonl]

Ok. After cloning, you can switch to that branch by running git checkout NonPrimaryDedup.

[cbostwick87]

I edited my previous comment, but I'm not sure it was seen. I used the command:
git clone https://github.com/statgen/bamUtil.git
cd bamUtil
make LIB_PATH_GENERAL=/topmed_variant_calling/libStatGen/ INSTALLDIR=.
to make the NonPrimaryDedup branch bamUtil.
I tried to use the bam dedup --recab command as above, but it returned exactly the same errors (trying both reference genomes) as before.

[jonathonl]

I cannot reproduce (see below). Can you try using test/testFiles/sortedBam1.bam as input? You could also try deleting /ref/hs38DH-bs.umfa. It may be corrupted and will be regenerated automatically once deleted.

$ bin/bam dedup --recab --in test/testFiles/sortedBam1.bam --out sortedBam1.bam.recab --force --refFile ../test_resources/resources/ref/hs38DH.fa --dbsnp ../test_resources/resources/ref/dbsnp_142.b38.vcf.gz --oneChrom --storeQualTag OQ --maxBaseQual 40
Creating FASTA binary cache file '../test_resources/resources/ref/hs38DH-bs.umfa'.
FASTA binary cache file '../test_resources/resources/ref/hs38DH-bs.umfa' created.
Load dbSNP file '../test_resources/resources/ref/dbsnp_142.b38.vcf.gz': (as text file) DONE!

[cbostwick87]

Hi, thank you and sorry I took so long to respond.
I tested the sortedBam1.bam file and got the same error about the reference genome. I then tried deleting the .umfa file and created a new one using the NonPrimaryDedup branch bamUtil. Using this new .umfa file, I was able to successfully run the dedup and recalibration steps on the test bam and my own files! So it would seem that perhaps the /ref/hs38DH-bs.umfa file was indeed corrupted as you suggested. Thank you so much for your help!