metaSPADES not producing contigs.fasta for certain samples

[kdbchau]

Hi,

Just wondering if it is normal for some samples to fail at producing output files such as contigs.fasta with metaspades? Out of 180 samples, 5 of them continue to not produce anything and there is not error coming up. The log files are produced but no contigs, and these 5 samples aren't different from the other samples in terms of size and number of sequences. I am using Illumina paired end reads for this. Is it possible that in these samples, the kmers are just not able to converge to create contigs? What could be causing the issue?

[kdbchau]

Actually, digging into the log files I do see an error but it is unclear to me. It says:

== Error == system call for: "['/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/spades/3.15.1/bin/spades-hammer', '/scratch/chauk/metaspades/sample_21_metagenome_results/corrected/configs/config.info']" finished abnormally, OS return value: -11

No idea what this error means. What happened?

[asl]

Will you please provide spades.log and params.txt files as you were instructed in the error message?

[kdbchau]

Here are my params.txt and spades.log files

params.txt spades.log

I also tried downloading spades 3.15 and compiling it from source. No difference. Issue still persists with the spades-hammer segmentation fault. I tried version 3.14 but it never ended, just got stuck for 2 days on nothing. Tried version 3.13. Same issue, segmentation fault.

The spades.log in this case gave me OS return value: 1. In other samples it gives return value -11.

[wuinqing]

#I had the same problem, metaSPADES not producing contigs.fasta. This is my running code:data/local/SPAdes-3.15.1-Linux/bin/metaspades.py --only-assembler --pe1-1 p1-4-8_trim1.clean.fq.gz --pe1-2 p1-4-8_trim2.clean.fq.gz -o #trimmomatic/p1-4-8/p1-4-8_trim_metaspades. The system says mimalloc error, unable to allocate OS memory (4194304 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1), finished abnormally, OS return value: -6.

[asl]

@wuinqing @parulbaranwal Please do not hijack other issues and open new ones using the instructions provided. Thanks!