Spades errors while trying to assemble low coverage genomes

[SilAdSe]

Description of bug

I am trying to assemble several low coverage spider genomes (2X-10X) with Spades using the following command: spades.py -1 ../File_1_paired.fq.gz -2 ../File_2_paired.fq.gz -t 20 -k 21,41,61,81,101,121 -o SpadesAssembly I started using Spades v3.12.0 for conda, and it worked quite good to assemble the first round of genomes. In a second round I started having problems with some assemblies, getting different kinds of errors, the most common being err -6 after the Starting k-mer counting step. I first thought it could be a problem of memory and I tried increasing the number of threads to increase the memory, but it didn't solve the problem, I also tried Spades v3.15.5 for conda and Spades v3.15.5 binaries for Linux. I have realized if I run the same job with the same parameters a a couple of times, the job reaches a different point each time, sometimes getting different errors (e.g. err -11, err -1), until in some of the cases one of the trials the job completes succesfully. I have read the spades.log files but I don't know how to interpret the errors. I wonder what is the problem, if it is the nature of the data, the parameters I am using or the server. I attach as an example log and params files of different trials for two of the data (DyguJL04ES and PterJL10ES) I have not managed to assemble yet. Thank you in advance. DyguJL04ES_4_spades.log DyguJL04ES_5_params.txt DyguJL04ES_5_spades.log PterJL10ES_1_params.txt PterJL10ES_1_spades.log PterJL10ES_2_params.txt PterJL10ES_2_spades.log PterJL10ES_3_params.txt PterJL10ES_3_spades.log PterJL10ES_4_params.txt PterJL10ES_4_spades.log DyguJL04ES_1_params.txt DyguJL04ES_1_spades.log DyguJL04ES_2_params.txt DyguJL04ES_2_spades.log DyguJL04ES_3_params.txt DyguJL04ES_3_spades.log DyguJL04ES_4_params.txt

spades.log

log.zip

params.txt

params.zip

SPAdes version

Spades v3.12.0 and Spades v3.15.5

Operating System

Server

Python Version

3.10.6

Method of SPAdes installation

conda and binaries

No errors reported in spades.log

• [X] Yes

[asl]

The problem likely stems from an I/O problem at your end as SPAdes intermediate files got corrupted. You might want to talk to your system administrator.

[SilAdSe]

Thank you very much!