Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-04T18:47:59.417Z
Comments.Text: When you say "SRA files", are these fastq? If these files are 'large', BLAST may not be the right tool for this
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-05T05:50:17.740Z
Comments.Text: @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.
Comments.UserDisplayName: Laura
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-06T23:47:10.263Z
Comments.Text: 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?
Comments.UserDisplayName: Kamil S Jaron
Tags: <blast><sratoolkit><sra>
Title: How to use SRA Toolkit to blast SRA accessions?
ThreadText: # 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**: @username_1 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?  
  
  ---
  
  ## 0 answers
  
  