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Remote BLAST retrieval crashes when NCBI result page does not contain <PRE> block #128

Description

@leonfaure

Environment:

  • CAGECAT 1.0
  • cblaster 1.4.1
  • remote mode
  • database: nr

Command used:

cblaster search \
  --output /repo/cagecat/jobs/I570I750O840E66/results/I570I750O840E66_summary.txt \
  --plot /repo/cagecat/jobs/I570I750O840E66/results/I570I750O840E66_plot.html \
  --blast_file /repo/cagecat/jobs/I570I750O840E66/results/I570I750O840E66_blasthits.txt \
  --mode remote \
  --database nr \
  --query_file cagecat/jobs/I570I750O840E66/uploads/genome_test.faa \
  --hitlist_size 10000 \
  --session_file /repo/cagecat/jobs/I570I750O840E66/results/I570I750O840E66_session.json \
  --max_evalue 0.01 \
  --min_identity 30 \
  --min_coverage 50 \
  --gap 20000 \
  --unique 3 \
  --min_hits 3 \
  --percentage 0 \
  --output_decimals 2 \
  --binary /repo/cagecat/jobs/I570I750O840E66/results/I570I750O840E66_binary.txt \
  --binary_decimals 2 \
  --binary_key len


Log:

[11:04:17] INFO - Starting cblaster in remote mode
[11:04:18] INFO - Request Identifier (RID): VRP1JKJZ014
...
[11:16:44] INFO - Search has completed successfully!
[11:16:44] INFO - Retrieving results for search VRP1JKJZ014
Traceback (most recent call last):
  File "/miniconda3/bin/cblaster", line 8, in <module>
    sys.exit(main())
  File "/miniconda3/lib/python3.9/site-packages/cblaster/main.py", line 432, in main
    cblaster(
  File "/miniconda3/lib/python3.9/site-packages/cblaster/main.py", line 318, in cblaster
    rid, results = remote.search(
  File "/miniconda3/lib/python3.9/site-packages/cblaster/remote.py", line 371, in search
    results = retrieve(rid, hitlist_size=hitlist_size)
  File "/miniconda3/lib/python3.9/site-packages/cblaster/remote.py", line 208, in retrieve
    for line in re.search("<PRE>(.+?)</PRE>", response.text, re.DOTALL)
AttributeError: 'NoneType' object has no attribute 'group'

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