Error during metaspades error correction only step-Finished abnormally, err code: 1

[cssulliv]

Hi,

I am currently using metaSPades v3.12 on our linux server and was running it only for error correction for 2 metagenomes. One of the genomes successfully got error corrected while the other one did not and I got the following error message below. I have also attached the params.txt and spades.log files for your reference. And am eager to understand /learn what the error message means.

params.txt spades.log

I have since then re-run metaspades for the other metagenome (running for 1 day now) and am also curious if error correction typically takes days to finish?

The program was terminated by segmentation fault
=== Stack Trace ===
[0x40a709]
[0x40a876]
[0x5b3220]
[0x48a3e4]
[0x441a3d]
[0x439b98]
[0x59a7ae]
[0x5ab8c4]
[0x60b969]


== Error ==  system call for: "['/home/cssulliv/Apps/metaspades3.12/share/spades-3.12.0-1/bin/spades-hammer', '/mnt/lts/nfs_fs02/pelagibacter_group/Clarisse/001_2011Samples/01_RAWDATA/16_SNV_ANALYSIS_ANVIO6.1_redo/From_Server/Amy_Smith_meta_raw_reads/spades_error_corrected_reads_sample_SRX742692/corrected/configs/config.info']" finished abnormally, err code: 1

Thank you in advance for the help :D

[asl]

Hello

Will you please give SPAdes 3.14 a try?

[cssulliv]

Hi @asl!

So I have been trying to install v3.14 using conda on our server but it was getting anaconda channel error messages even after adding the -c bioconda flag.

I used conda create -p /path/to/metaSPades3.14 -c bioconda spades=3.14.0-0 and I basically get a message saying that conda can't find it.

Happy to try to install it again if there is a work around that you can suggest :)

[asl]

We do not maintain conda packages. Maybe @notestaff knows

[notestaff]

Try conda create -p /path/to/metaSPades3.14 —override-channels -c comda-forge -c bioconda -c defaults spades=3.14.0