Entering edit mode
23 months ago
elin_smith
•
0
Trying to use blastn locally on terminal for the first time, but the output file is empty each time even though the process runs for over an hour. My query file is correct as well as my file pathing as far as I can tell. blastn version is ncbi-blast-2.13.0+
If anyone has any idea as to where I'm going wrong it would be much appreciated!!
Could you please try to run this on the command line and not through R? You might not capture all important error messages that way. Also, change -outfmt to 7 or 0 for your test run. An empty outfmt 6 file might mean no hits found.
Thanks for your help! I'll update once this run completes
I keep getting the error 'Segmentation fault:11' regardless of the -outfmt value. Could this be an issue with memory?
Could be many things, memory one of them, how much meomory do you have? Check the following: - run the same command with only a single query sequence, - check if you have the version of blast that is compiled for your OS and architecture (e.g. x86_64 vs arm), - how did you download the NT database, is it complete? - make a small nucleotide database with makeblastdb from a few of your query sequences and use this db for a test.
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