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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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Spades assembly crashed without log error #334

Open Fla1487 opened 1 month ago

Fla1487 commented 1 month ago

Dear All, I have a problem with unicylcer and short reads alignment by using spades. I have previously used the same command without any troubles. Now with new sequences, and old ones, unicycler crashs.

Unicycler version: v0.5.0 Using 16 threads

Dependencies: Program Version Status
spades.py 3.15.5 good
racon not used makeblastdb 2.14.1+ good
tblastn 2.14.1+ good

This is the generated error (I have checked the log file without finding anything):

Error: SPAdes encountered an error:

Could You help to identify the problem?

Thank you in advance

Fla1487 commented 1 month ago

I add also that follwoing uniclycler/spades guides, it is possible modify spades parameter, so that I added --spades options "-m 1024". Unfortunatly I obtained: unicycler: error: unrecognized arguments: --spades-options -m 1024

Honestly, I do not understand whats is the problem

Thank you again

pwkooij commented 4 weeks ago

@Fla1487 Not sure if it will resolve your problems, but I believe the correct argument should be --spades_options -m 1024

marrip commented 3 days ago

I have the same problem, did not try the option though...