Comments (4)
Hi there,
Command exit status:
137
seems to indicate that more memory than allowed was used. 16.GB
memory seems also not a lot and likely leads to more problems downstream. I assume the number of reads already crushes DADA2_QUALITY. Just to try where you come to your next bottleneck, you can try --skip_dada_quality.
Most likely unrelated:
- I have no idea what pipeline version
-r 306ad5df8f
refers to, if using a release,-r 2.6.1
would be more verbose. - Your nextflow version looks a little old, maybe you could update (2.6.1 requires 23.04 or such)
Unrelated: --trunclenf 200 --trunclenr 140 --illumina_pe_its
are not really supposed to use together, they seem to overwrite each other. Probably you rather want to use --double_primer
?
from ampliseq.
Hi,
thanks for the quick reply.
Jun-28 12:16:54.774 [main] INFO nextflow.cli.CmdRun - Launching
https://github.com/nf-core/ampliseq` [deadly_hugle] DSL2 - revision: 306ad5d [2.3.1]`
So I assume it is version 2.3.1
The thing is I am running the container within a research computing environment provided by the institution I work for and those were the maximum values for mem and cpus, but absolutely they are low. I will check how I can increase, as well as to install a newer version of nextflow.
As for the parameters, I will check them in a bit more detail, I just took this project over from a colleague
from ampliseq.
Well, 2.3.2 fixed a bug with DADA2_QUALITY, see https://github.com/nf-core/ampliseq/releases/tag/2.3.2, might help. Those releases are already quite old, maybe you could update?
from ampliseq.
I close that now because there wasnt any response, so I assume it was solved.
from ampliseq.
Related Issues (20)
- ERROR: R_HOME ('/usr/local/lib/R') not found HOT 5
- Misleading error message when samples are not passing filterandtrim HOT 1
- Accessing 16S gene identifiers HOT 13
- DADA2 split regions singularity HOT 13
- multi-region analysis: sidle/reconstructed/reconstructed_merged.tsv OCCATIONALLY mis-formatted HOT 1
- Running test error HOT 1
- Abundance plots for qiime2 results without metadata provided HOT 3
- Adding ONT read support for ampliseq HOT 2
- `overall_summary.tsv` sometimes with misleading numbers in 2.9.0 HOT 11
- Analyse data set that contains unknown primer set HOT 5
- Cutadapt with "-u" instead of "fw/rv_primer seq" HOT 1
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- Misleading text in output documentation HOT 1
- Add MACSE to enable frame-shift detection for COI HOT 6
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- Error "Can't stage file https://files.plutof.ut.ee:" Download fail HOT 7
- Taxonomy database choices not validated against permitted values since 2.9.0 HOT 3
- New (10.0) version of Unite databases available to `--dada_ref_taxonomy`
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from ampliseq.