search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
737 stars 135 forks source link

What is error code -11? #246

Open crysclitheroe opened 5 years ago

crysclitheroe commented 5 years ago

Good Day

Is this error a memory problem? On Linux cluster, (max 600GB mem, 4 nodes, 8 cpuspernode) I also get error code -11 on SPAdes 3.13.0:

== Error == system call for: "['/work/.apps/free72/SPAdes/3.13.0/bin/spades-core', '/path/to/assembly/K77/configs/config.info']" finished abnormally, err code: -11

on the "hybrid_aligning.cpp" step for k77 (eukaryotic de novo assembly using long (2.7GB nanopore) and short reads (120GB, paired-end Illumina, carefully cleaned)); 4:42:39.180 59G / 85G INFO General (hybrid_aligning.cpp : 268) Prepared batch 0 of 50000 reads.

Several runs have failed in a similar way for the same data. Please find attached the log files for most recent run. params.txt spades.log

I will try spades 3.11.1 in the mean time.

Thanks and kind regards Crystal

asl commented 5 years ago

No, it seems to be a "proper" crash.

In order to reproduce & fix the issue we need your input files. Will it be possible to arrange?

crysclitheroe commented 5 years ago

Dear asl

Thanks for getting back to me. I might be able to do that (the files are quite large and will take a day or two to upload), but first I need to talk about it with PI who is away right now. In the mean time Im trying both on a different memory partition (apparently some of our clusters nodes were failing) and a different version of spades. So far, everything is running. Will get back to you later.

Thanks and kind regards crystal

crysclitheroe commented 5 years ago

Dear @asl

My PI is happy to share the input files, but please don't share the data. Do you have an email address I can send the Data to (you can mail me at crystal.clitheroe@oist.jp)? What all do you need, input files and bashscript and/or spades.log and partially run output folders?

Thanks again for you help. Crystal

asl commented 5 years ago

Great news, thanks!

You could email us at spades.support@cab.spbu.ru. Let's proceed over the email about what will be necessary.