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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Error == system call for: config.info #1331

Open anaalmeidasantos opened 2 months ago

anaalmeidasantos commented 2 months ago

Description of bug

I was running Unicycler to assemble a hybrid genome and encountered the following error related to SPAdes:

WARNING: Try to use logger before create one. Level=ERROR. Message=File /hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info doesn't exist or can't be read!

== Error == system call for: "['/hpc/dla_mm/anasantos/data/miniconda3/envs/unicycler_env/bin/spades-core', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/isolate_mode.info']" finished abnormally, OS return value: 2

I do not know what this is about. I usually do this all the time and never got this error before.

Could You help to identify the problem?

Thank you in advance

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.4

Operating System

I am using a server (HPC)

Python Version

No response

Method of SPAdes installation

conda

No errors reported in spades.log

asl commented 2 months ago

Could You help to identify the problem?

There are no errors in attached spades.log file. Will you please attach a correct one from failed run?

anaalmeidasantos commented 2 months ago

It is the correct file.

The error is: == Error == system call for: "['/hpc/dla_mm/anasantos/data/miniconda3/envs/unicycler_env/bin/spades-core', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/isolate_mode.info']" finished abnormally, OS return value: 2

asl commented 2 months ago

Looks like you redirected output from several runs into a single output directory – spades.log contains intermixed lines. This is not going to work.

anaalmeidasantos commented 2 months ago

I only did:

unicycler -1 namefile_1.fastq.gz -2 namefile_2.fastq.gz -l namefile.fastq -o name_of_directory