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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Error code 2. unlink(2) failed #1347

Closed Abeersohrab closed 3 months ago

Abeersohrab commented 3 months ago

I have been trying to run spades and it keeps stopping with an unlink(2) failed. Reason: No such file or directory. Error code: 2. File:/scratch/general/nfs1/u1370694/spades_output1/tmp/spades_fykgm5pp/construction_TDu9oM/kmers_raw_jTMlEL.189

== Error == system call for: "['/uufs/chpc.utah.edu/sys/installdir/r8/spades/3.15.4/bin/spades-core', '/scratch/general/nfs1/u1370694/spades_output1/K21/configs/config.info', '/scratch/general/nfs1/u1370694/spades_output1/K21/configs/mda_mode.info', '/scratch/general/nfs1/u1370694/spades_output1/K21/configs/meta_mode.info']" finished abnormally, OS return value: 2 None params.txt spades.log

asl commented 3 months ago

This is an I/O problem on your end likely caused by malfunctioning of storage system (SPAdes cannot delete one of its intermediate files). I would suggest you to ask your system administrator.