Makeblastdb: Job output not returned from cluster error

Hello, I am using the web-based GALAXY and I converted FASTQ files to FASTA and I am attempting to construct a BLAST database from these newly formed FASTA files.

As I use the makeblastdb function in Galaxy, I get an error message saying “Job output not returned from cluster error”. Has anyone experienced this before? If so, I would appreciate any possible solutions to this.

Thank you.

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Hi @R_J

A fasta dataset created from a fastq dataset usually contains too many sequences to index. Thousands are Ok, millions are not.

What to do:

  1. Try at least one rerun to eliminate server issues
  2. Check the fasta data format Datatypes - Galaxy Community Hub
  3. Check the tool form settings. Example: “Molecule type of input” – that should be toggled to be “nucleotide”. Other settings should probably be left at the default.
  4. If all that is correct, and the tool still fails, then it is too large and you may need to assemble the sequences before using them as a target BLAST database.


I linked some prior Q&A that is related – click on the tags to review.

Hope that helps!

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For this specific error, please rerun the tool. If it still crashes, please send an error report to inform the Admins.

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Hey @jennaj , thank you so much for your input. I believe the file was too large and dealing with that I was able to overcome this error. Thank you!

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