Warning: Reading will be unbuffered.
Answered
Hello!
I am trying to use liftover a vcf file from hg19 to hg38. I don't get any error messages but I do get warning messages that confuse me.
a) GATK version used: gatk-4.1.8.0
b) Exact GATK commands used
gatk LiftoverVcf
-I CS39Trio.vcf
-O CS39Triohg38.vcf
-CHAIN hg19ToHg38.over.chain
-REJECT CS39Triohg38Reject.vcf
-R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta
c) The entire error log if applicable.
There is no error log but I do get the following warnings:
WARNING 2020-07-06 12:12:45 LiftoverVcf 23454 variants with a swapped REF/ALT were identified, but were not re covered. See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO 2020-07-06 12:12:48 LiftoverVcf Writing out sorted records to final VCF.
WARNING 2020-07-06 12:12:49 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
What do these warnings mean? I am working on SSH. How do I fix the the problem?
Thank you in advance!
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Hi Linda Do
You don't need to worry about warnings. They do not effect your analysis or results. It's just giving you more information on what's going on under the hood. If you want more info on this,as mentioned in the warning message, see RECOVER_SWAPPED_REF_ALT and associated caveats in the tool docs: https://gatk.broadinstitute.org/hc/en-us/articles/360045682651-LiftoverVcf-Picard-
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this warning, saying unbuffered etc, will cause all procedure very very slow, as much fewer memory will be occupied.
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Thank you for answers!
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