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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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finished abnormally, OS return value: -11 #1072

Open Soumyadutta-basak opened 1 year ago

Soumyadutta-basak commented 1 year ago

Description of bug

Hey I have been trying to run spades This is the command i used

spades.py --only-assembler -o SPADES_OUT -1 S17_Trimmed_R1.fq.gz -1 S46_Trimmed_R1.fq.gz -1 S62_Trimmed_R1.fq.gz -1 S72_Trimmed_R1.fq.gz -1 S81_Trimmed_R1.fq.gz -2 S17_Trimmed_R2.fq.gz -2 S46_Trimmed_R2.fq.gz -2 S62_Trimmed_R2.fq.gz -2 S72_Trimmed_R2.fq.gz -2 S81_Trimmed_R2.fq.gz

I got the error message as shown below ending the spades.py running: == Error == system call for: "['/tools/spades/bin/spades-core', '/home/sandeeplab1/WGS_fungi/3_Assembly/SPADES_OUT/K21/configs/config.info']" finished abnormally, OS return value: -11

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes genome assembler v3.15.5

Operating System

Ubuntu 22.04.1

Python Version

No response

Method of SPAdes installation

manual

No errors reported in spades.log

asl commented 1 year ago

How much free RAM is available for your SPAdes job? Does spades.py --test run properly?

Soumyadutta-basak commented 1 year ago

Yes i tried spades.py --test but its still showing the same error

= Error == system call for: "['/tools/spades/bin/spades-hammer', '/home/sandeeplab1/WGS_fungi/3_Assembly/spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -11

spades.log params.txt

asl commented 1 year ago

I'd suspect there is some I/O issue on the volume that your /home is located. Maybe it does not support memory-mapped files properly. I would suggest you to talk to your system administrator.

Soumyadutta-basak commented 1 year ago

I re-installed SPAdes and its working fine now. Thank you so much for helping.

SowmyaPulapet commented 1 year ago

Hi @Soumyadutta-basak , Would you please tell me how did you solve this issue ? I am also facing the same issue.

crockydavr commented 1 year ago

Hi @Soumyadutta-basak , Would you please tell me how did you solve this issue ? I am also facing the same issue.

I managed to solve this problem by compiling. The manual describes in detail what is needed for it.

SowmyaPulapet commented 1 year ago

Oh okay, Thank you. @crockydavr