Denoising Error

Hi all, hoping someone can help me troubleshoot this error. Here is the script I ran:

#!/bin/bash
#SBATCH -o /home/areaume/scripts/slurmout/slurm-%j.out # STDOUT
module load miniconda
source activate qiime2-2023.2
qiime dada2 denoise-paired
--i-demultiplexed-seqs /home/areaume/Chapter1/16SCh1/trimmed-samples.qza
--p-trunc-len-f 295 --p-trunc-len-r 275
--p-n-threads 18
--o-denoising-stats /home/areaume/Chapter1/16SCh1/dns
--o-table /home/areaume/Chapter1/16SCh1/table
--o-representative-sequences /home/areaume/Chapter1/16SCh1/rep-seqs
--verbose
qiime metadata tabulate
--m-input-file /home/areaume/Chapter1/16SCh1/dns.qza
--o-visualization /home/areaume/Chapter1/16SCh1/dns
qiime feature-table tabulate-seqs
--i-data /home/areaume/Chapter1/16SCh1/rep-seqs.qza
--o-visualization /home/areaume/Chapter1/16SCh1/rep-seqs
qiime feature-table summarize
--i-table table.qza
--m-sample-metadata-file Ch1Metadata_16S.tsv
--o-visualization table

I've attached the output message as well as my demux summarize .qzv file for the input sequences.

Thanks in advance!

slurm-428312.txt (7.2 KB)
trimmedQC.qzv (320.8 KB)

I did a little more searching today and found the answer here! It was a memory issue. I had to decrease the number of threads.

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Hi @areaume,

In the slurm file at the bottom there is this message:

There was a problem with the command:
(1/1) Invalid value for '--i-data': /home/areaume/Chapter1/16SCh1/rep-
seqs.qza does not exist.
There was an issue with loading the file Ch1Metadata_16S.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): Ch1Metadata_16S.tsv

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: Metadata in QIIME 2 — QIIME 2 2023.2.0 documentation

slurmstepd: error: Detected 909 oom-kill event(s) in StepId=428312.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.

Let start at the top of this message which indicates that there was a problem loading the metadata, can you double check that all the file paths in your commands are correct and re run your commands again? If that doesn't work we can keep working through it!

-Hannah

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@areaume,
Glad you were able to figure it out!

Ah yes, that was the second issue. I fixed the path after reducing the threads and it's all working out now!

1 Like