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nf-core / mag

Assembly and binning of metagenomes
https://nf-co.re/mag
MIT License
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Pipeline completed sucessfully, but with errored process(es) #610

Closed Anenovaes closed 2 months ago

Anenovaes commented 2 months ago

Description of the bug

I successfully ran the pipeline; however, some processes did not execute, resulting in a failure in the MAGBIN2 process. copyscreenshot

The .command.log indicates:

WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
MaxBin 2.2.7
Input contig: input/MEGAHIT-magmax01.contigs.fa
Located abundance file [magmax01_mb2_depth.txt]
Thread: 6
out header: MEGAHIT-MaxBin2-magmax01
Searching against 107 marker genes to find starting seed contigs for [input/MEGAHIT-magmax01.contigs.fa]...
Running FragGeneScan....
Running HMMER hmmsearch....
Try harder to dig out marker genes from contigs.
Marker gene search reveals that the dataset cannot be binned (the medium of marker gene number <= 1). Program stop.

Despite running the pipeline with different sets of files, I consistently obtained the same results. Additionally, when attempting to parse more than one file as input, only one file was processed in the pipeline.

Command used and terminal output

nextflow run nf-core/mag -profile singularity --input /path/to/input_files/*.fastq.gz --outdir /path/to/output_dir --single_end --/path/to/host_reference --busco_db /data/busco/busco_downloads --busco_clean --run_virus_identification -resume

Relevant files

No response

System information

Nextflow version: 23.10.1 Executor: local/server Container engine: Singularity OS: Ubuntu 22.04.2 LTS Version of nf-core/mag: v2.5.4

jfy133 commented 2 months ago

The errored process is fine and does not represent a failure of the pipeline. Unfortuantey MaxBIN2 fails entirely if it 'just' finds no bins, rather than just completing successfully and reporting 'no bins found'. So in a weird way 'you don't have to worry'.

For the single file being run, I suspect this is because you've not wrapped the --input path and glob in a quotes:

--input '/path/to/input_files/*.fastq.gz'

Should then allow nextflow to evalute teh glob rather than bash :)