disable the SRA cache in HISAT2
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3.9 years ago
Chvatil ▴ 130

Hello, I found many posts talking about this subject but none of them explain how to do that.

In fact I ran a HISAT2 analysis on my data, for that I use the --sra-acc option with the sra IDS.

Then I map these read against a fasta genome assembly. But during the process I get this error message :

VCursorCellDataDirect failed: '(INSDC:quality:phred)QUALITY' [1351681] rc = RC(rcNS,rcFile,rcReading,rcNoObj,rcIncomplete)
An error happened while fetching SRA reads. Please rerun HISAT2. You may want to disable the SRA cache if you didn't (see the instructions at https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration).
(ERR): hisat2-align exited with value 1
[bam_sort_core] merging from 44 files and 1 in-memory blocks...

I tried to disable the cache bu using the command :

vdb-config -i

But I get the following message :

2020-06-27T10:48:57 vdb-config.2.3.5 err: param unknown while parsing argument list within application support module - Unknown argument '-i'
2020-06-27T10:48:57 vdb-config.2.3.5 err: param unknown while parsing argument list within application support module - While calling ArgsMakeAndHandle

does someone have an idea to disable the SRA cache ? Thanks for your time

hisat rnaseq mapping • 1.1k views
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