<p>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.</p>
<pre><code>module load anaconda3/personal
source activate sratoolkit

cd ~/sra-tools
PATH=$PATH:~/sra-tools/sratoolkit.2.10.5-ubuntu64/bin
tblastn_vdb -db &quot;SRR6256958&quot; -query ~/sra-tools/query/query.txt -out ~/sra-tools/out/results.txt
</code></pre>
<p>I get nothing in my output file except for 'TBLASTN 2.6.1+'. My error file goes as follows:</p>
<pre><code>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 &quot;/panfs/pan1/sra-test/vdb3/git/blast_vdb/sratoolkit_2_9_0/c++/src/algo/blast/api/prelim_stage.cpp&quot;, 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]
</code></pre>
<p>Does anyone know what I am doing wrong? Help would be much appreciated!</p>

CC BY-SA 4.0
2021-08-04T18:47:59.417Z
When you say "SRA files", are these fastq? If these files are 'large', BLAST may not be the right tool for this
Chris_Rands
CC BY-SA 4.0
2021-08-05T05:50:17.740Z
@Chris_Rands No particular format at the moment since I haven't downloaded them separately. It was supposed to happen automatically? There should be enough space at least for this first file (8.79 gigabases), but the download doesn't even start.
Laura
CC BY-SA 4.0
2021-08-06T23:47:10.263Z
SRA contains raw sequencing reads, blast usually serves in aligning genes / parts of genomes / assembled sequences (not sequencing reads). But I don't know `tblastn_vdb`. You sure the command is supposed to do what you think it should?
Kamil S Jaron
<blast><sratoolkit><sra>
How to use SRA Toolkit to blast SRA accessions?
# How to use SRA Toolkit to blast SRA accessions?

(Asked by: username_0 on 2021-08-04)

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!

**Tags:** blast, sratoolkit, sra
> **Comments:**
> **username_1**: When you say "SRA files", are these fastq? If these files are 'large', BLAST may not be the right tool for this  
> **username_0**: @Chris_Rands No particular format at the moment since I haven't downloaded them separately. It was supposed to happen automatically? There should be enough space at least for this first file (8.79 gigabases), but the download doesn't even start.  
> **username_2**: SRA contains raw sequencing reads, blast usually serves in aligning genes / parts of genomes / assembled sequences (not sequencing reads). But I don't know `tblastn_vdb`. You sure the command is supposed to do what you think it should?  

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## 0 answers

