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Hi all - I'm running into the following error with...
# ampliseq
e
Hi all - I'm running into the following error with ampliseq. Has anyone seen this before? I'm working with nextflow v24.04.4 but also get this error with an older version. I'll paste the full script in the comments. If I navigate to the work folder list below, I do see the .svg files ampliseq says it can't find. 
Quitting from lines 358-363 [unnamed-chunk-14] (template.Rmd)
`Error in `knitr::include_graphics()`:` 
! Cannot find the file(s): "FW_preprocessed_qual_stats.svg"; "RV_preprocessed_qual_stats.svg"
Backtrace:
1. knitr::include_graphics(c(params$dada_pp_qc_f_path, params$dada_pp_qc_r_path))
Execution halted Work dir:
/work/gmgi/Fisheries/eDNA/NY/scripts/work/b9/6d929f5af591fd5f62c7608e4c6691
`Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`` 
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>
-- Check '.nextflow.log' file for details
Copy code
#!/bin/bash
#SBATCH --error=output_messages/"%x_error.%j" #if your job fails, the error report will be put in this file
#SBATCH --output=output_messages/"%x_output.%j" #once your job is completed, any final job report comments will be put in this file
#SBATCH --partition=short
#SBATCH --nodes=1
#SBATCH --time=20:00:00
#SBATCH --job-name=ampliseq
#SBATCH --mem=70GB
#SBATCH --ntasks=24
#SBATCH --cpus-per-task=2

## LOAD CONDA ENV
source ~/../../work/gmgi/miniconda3/bin/activate
conda activate nextflow

# SET PATHS
metadata="/work/gmgi/Fisheries/eDNA/NY/metadata"
output_dir="/work/gmgi/Fisheries/eDNA/NY/results"
nextflow run nf-core/ampliseq \
   -profile singularity \
   --input ${metadata}/samplesheet.csv \
   --FW_primer "GTCGGTAAAACTCGTGCCAGC" \
   --RV_primer "CATAGTGGGGTATCTAATCCCAGTTTG" \
   --outdir ${output_dir} \
   --trunclenf 20 \
   --trunclenr 20 \
   --trunc_qmin 25 \
   --max_len 200 \
   --max_ee 2 \
   --sample_inference pseudo \
   --skip_taxonomy \
   --ignore_failed_filtering  \
   --ignore_failed_trimming
d
I have no idea, but those are incredibly short truncation lengths. The lengths will be what the pipeline cuts down the reads to after first removing the primers, i.e. the length of the useful sequence. Your forward primer is 21 and your reverse 27, so this makes a total of 41 and 47 -- you surely sequence more than that, right? Moreover, 
--trunc_qmin
doesn't do anything (AFAIK) when the lengths are set.
Which version of the pipeline?
Another thing, normally with a slurm cluster you would run with 
-profile slurm,singularity
to let Nextflow take care of job submission. This is more effective as it can utilize more than one compute node.
🙌 1
e
Ah! Thank you, that is meant to be 200 in both spots not 20. I re-ran and this is working again
🙌
d
Perfect!
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