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How to use SRA Toolkit to blast SRA accessions?

Bioinformatics Asked on August 11, 2021

I’m trying to look for a gene in a group of SRA files. Web BLAST can’t cope with them, so I assume they’re too large. I’ve tried tblastn_vdb from the SRA toolkit, as follows. It had previously worked well for me for WGS files.

module load anaconda3/personal
source activate sratoolkit

cd ~/sra-tools
PATH=$PATH:~/sra-tools/sratoolkit.2.10.5-ubuntu64/bin
tblastn_vdb -db "SRR6256958" -query ~/sra-tools/query/query.txt -out ~/sra-tools/out/results.txt

I get nothing in my output file except for ‘TBLASTN 2.6.1+’. My error file goes as follows:

Loading anaconda3/personal
  Loading requirement: fix_unwritable_tmp fix_setxattr
VDB: 2021-07-16T12:03:22 . debug: KSysDirResolvePath_v1 = '/[path]/sra-tools/sratoolkit.2.10.5-ubuntu64/schema'
VDB: 2021-07-16T12:03:22 . debug: KSysDirResolvePath_v1 = '/tmp/pbs.4070476.pbs'
VDB: 2021-07-16T12:03:22 . debug: KSysDirResolvePath_v1 = '/tmp/pbs.4070476.pbs'
BLAST engine error: NCBI C++ Exception:
    T0 "/panfs/pan1/sra-test/vdb3/git/blast_vdb/sratoolkit_2_9_0/c++/src/algo/blast/api/prelim_stage.cpp", line 304: Error: BLAST::ncbi::blast::CBlastPrelimSearch::Run() - search cannot proceed due to errors retrieving sequences from databases

/var/spool/PBS/mom_priv/jobs/4070476.pbs.SC: line 7: 4032551 Aborted [then it lists the original code again]

Does anyone know what I am doing wrong? Help would be much appreciated!

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