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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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OS return value: -7 #1018

Open MoriatyZy opened 2 years ago

MoriatyZy commented 2 years ago

Description of bug

I'm trying to assemble some viral sequences. Spades finished with OS return value: -7 Running with pair-end input

Besides, when I trying to test using _spades.py --test__, a warning came up as follows: ======= SPAdes pipeline finished WITH WARNINGS!

=== Error correction and assembling warnings:

spades.log

[Uploading spades.log…]()

params.txt

params.txt

SPAdes version

SPAdes v 3.15.5

Operating System

Linux 3.10.0-1062.el7.x86_64

Python Version

3.7.12

Method of SPAdes installation

conda

No errors reported in spades.log

asl commented 2 years ago

Please upload spades.log file as your were instructed in the issue / error message

MoriatyZy commented 2 years ago

spades.log

Oh, very sorry, it didn't upload successfully before

asl commented 2 years ago

This looks like an I/O problem. Does the problem reproduce with the restart?

MoriatyZy commented 2 years ago

I retried with the same data (sample: H1) , and I also tested with a very small fastq file with the same commands and parameters. I found that the test result was normal but the sequences of H1 assembly still failed.

spadestest.log spadesH1.log

ReemaSingh commented 1 year ago

I am also getting the "finished abnormally, OS return value: -7" error. Please see the complete error below in the attached spades log. I don't think it is a RAM problem because I have already provided it with 500 GB RAM. I would highly appreciate any response on this. spades.log

ReemaSingh commented 1 year ago

Just a quick follow-up on my previous message. The error solved when I rerun rnaSPADES with --memory 1500 parameter

ReemaSingh commented 1 year ago

Again getting the same error. I provided 1500 RAM and when I get the error the program was using only 169 GB of ram.

89/169G INFO UnbranchingPathExtractor (debruijn_graph_constructor:354) Extracting unbranching paths

== Error == system call for: "['SPAdes-3.15.5-Linux/bin/spades-core', Assembly/K49/configs/config.info, Assembly/K49/configs/mda_mode.info, Assembly/K49/configs/rna_mode.info']" finished abnormally, OS return value: -7

I would appreciate any response

neolycus23 commented 7 months ago

Again getting the same error. I provided 1500 RAM and when I get the error the program was using only 169 GB of ram.

89/169G INFO UnbranchingPathExtractor (debruijn_graph_constructor:354) Extracting unbranching paths

== Error == system call for: "['SPAdes-3.15.5-Linux/bin/spades-core', Assembly/K49/configs/config.info, Assembly/K49/configs/mda_mode.info, Assembly/K49/configs/rna_mode.info']" finished abnormally, OS return value: -7

I would appreciate any response

@ReemaSingh did you find a solution to this problem?

ReemaSingh commented 7 months ago

Again getting the same error. I provided 1500 RAM and when I got the error the program was using only 169 GB of ram.

89/169G INFO UnbranchingPathExtractor (debruijn_graph_constructor:354) Extracting unbranching paths

== Error == system call for: "['SPAdes-3.15.5-Linux/bin/spades-core', Assembly/K49/configs/config.info, Assembly/K49/configs/mda_mode.info, Assembly/K49/configs/rna_mode.info']" finished abnormally, OS return value: -7

I would appreciate any response

@ReemaSingh did you find a solution to this problem?

@neolycus23, I rerun these samples after cleaning them using Kraken2. The run failed again with a new error message “I/O error! Incomplete write! Reason: Input/output error. Error code:5”. As all of my input files were ok so I talked to our system admin and he mentioned that it could be due to transient network issues and I should resubmit the job. Finally, I rerun the job and it worked this time 😄