Process spades (Q) terminated with an error exit status (1)

[sajjadasaf]

Dear Kevin,
I have run hybrid assembly with docker by following commands but it ended with an error.
Could you help me to find out is it memory error or something else.

(base) ThinkStation-P910:/data$ nextflow run kevinmenden/hybrid-assembly -profile docker --shortReads '*_R{1,2}.fastq.gz' --longReads combinedall.fastq --assembler spades
executor > local (3)
[8e/a9bc99] process > get_software_versions [100%] 1 of 1 ✔
[0e/54207c] process > fastqc (Q) [100%] 1 of 1 ✔
[5a/190f77] process > spades (Q) [ 0%] 0 of 1
[- ] process > quast_spades -
[- ] process > multiqc -
Error executing process > 'spades (Q)'

Caused by:
Process spades (Q) terminated with an error exit status (1)

Command executed:

spades.py -o "spades_results" -t 16
-m 700
-1 Q_R1.fastq.gz -2 Q_R2.fastq.gz
--nanopore combinedall.fastq
-k 21,33,55,77
mv spades_results/scaffolds.fasta scaffolds.fasta
mv spades_results/contigs.fasta contigs.fasta

Command exit status:
1
.
.
.
.
.

== Error == system call for: "['/opt/conda/envs/assembly-env/share/spades-3.12.0-1/bin/spades-hammer', 'spades_results/corrected/configs/config.info']" finished abnormally, err code: -9

In case you have troubles running SPAdes, you can write to [email protected]
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.

Work dir:
/media/laptop/zygopyllumtest/Q1 data/work/5a/190f77d2679c458bba66b2142565a1

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[KevinMenden]

Hi,

it's not really possible to debug this for me, unfortunately.
Please check for nextflow log files (.nextflow.log) in the directory, and then also check the files mentioned by the error message (params.txt and spades.log) to see what is going on. Otherwise it's not possible to say.

Best,
Kevin