d4straub
commented
1 year ago Hi there!
Unfortunately you run the pipeline in a non-recommended way and therefore I can hardly be of any assistance. The problem to me is that you do not use any -profile such as -profile conda or -profile singularity which would make you use the software that is shipped with the pipeline. See https://nf-co.re/usage/introduction#how-to-run-a-pipeline. Instead you seem to install all software yourself and start the pipeline in that custom software environment? That makes troubleshooting close to impossible.
linshizuowei
Description of the bug
Hi, when I add --picrust2 parameter in nextflow command, thers is an error occured, "Process
NFCORE_AMPLISEQ:AMPLISEQ:PICRUST (rep-seq.fasta,feature-table.tsv)terminated with an error exit status (1)" but there is no detailed error message，Is this an error about gappa ? detailed info of .nextflow.log is described below any help would be greatly appreciated. Thank youCommand used and terminal output
Relevant files
" task: name=NFCORE_AMPLISEQ:AMPLISEQ:PICRUST (rep-seq.fasta,feature-table.tsv); work-dir=/data1/zhangjinxin/3/work/23/a845460a864d3d91c5183cd7658a05 error [nextflow.exception.ProcessFailedException]: Process NFCORE_AMPLISEQ:AMPLISEQ:PICRUST (rep-seq.fasta,feature-table.tsv) terminated with an error exit status (1) 5月-15 07:51:04.640 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:PICRUST (rep-seq.fasta,feature-table.tsv)'
Caused by: Process NFCORE_AMPLISEQ:AMPLISEQ:PICRUST (rep-seq.fasta,feature-table.tsv) terminated with an error exit status (1)
Command executed:
If input is QIIME2 file, than (1) the first line and (2) the first character (#) of the second line need to be removed
if [ "QIIME2" == 'QIIME2' ] then tail -n +2 "feature-table.tsv" > "feature-table.tsv.tmp" && mv "feature-table.tsv.tmp" "feature-table.tsv" fi
picrust2_pipeline.py -t epa-ng --remove_intermediate -s rep-seq.fasta -i feature-table.tsv -o all_output -p 6 --in_traits EC,KO --verbose
Add descriptions to identifiers
add_descriptions.py -i all_output/EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -m EC -o EC_pred_metagenome_unstrat_descrip.tsv add_descriptions.py -i all_output/KO_metagenome_out/pred_metagenome_unstrat.tsv.gz -m KO -o KO_pred_metagenome_unstrat_descrip.tsv add_descriptions.py -i all_output/pathways_out/path_abun_unstrat.tsv.gz -m METACYC -o METACYC_path_abun_unstrat_descrip.tsv
echo "This Picrust2 analysis is based on filtered reads from QIIME2" > "This Picrust2 analysis is based on filtered reads from QIIME2.txt" echo -e "picrust -t epa-ng --remove_intermediate" > "picrust.args.txt"
cat <<-END_VERSIONS > versions.yml "NFCORE_AMPLISEQ:AMPLISEQ:PICRUST": python: $(python --version 2>&1 | sed 's/Python //g') picrust2: $( picrust2_pipeline.py -v | sed -e "s/picrust2_pipeline.py //g" ) END_VERSIONS
Command exit status: 1
Command output: INFO Time spent placing: 38s INFO Elapsed Time: 52s
Invocation: gappa examine graft --jplace-path /tmp/tmp8uspczvl/epa_out/epa_result_parsed.jplace --fully-resolve --out-dir /tmp/tmp8uspczvl/epa_out Command: gappa examine graft
Input: --jplace-path /tmp/tmp8uspczvl/epa_out/epa_result_parsed.jplace
Settings: --fully-resolve true --name-prefix
Output: --out-dir /tmp/tmp8uspczvl/epa_out --file-prefix --file-suffix
Newick Tree Output: --newick-tree-quote-invalid-chars false
Global Options: --allow-file-overwriting false --verbose false --threads 88 --log-file
Run the following command to get the references that need to be cited: gappa tools citation Czech2020-genesis-and-gappa
Started 2023-05-15 19:51:02
Found 1 jplace file
Finished 2023-05-15 19:51:02
Command error: INFO Time spent placing: 38s INFO Elapsed Time: 52s
Invocation: gappa examine graft --jplace-path /tmp/tmp8uspczvl/epa_out/epa_result_parsed.jplace --fully-resolve --out-dir /tmp/tmp8uspczvl/epa_out Command: gappa examine graft
Input: --jplace-path /tmp/tmp8uspczvl/epa_out/epa_result_parsed.jplace
Settings: --fully-resolve true --name-prefix
Output: --out-dir /tmp/tmp8uspczvl/epa_out --file-prefix --file-suffix
Newick Tree Output: --newick-tree-quote-invalid-chars false
Global Options: --allow-file-overwriting false --verbose false --threads 88 --log-file
Run the following command to get the references that need to be cited: gappa tools citation Czech2020-genesis-and-gappa
Started 2023-05-15 19:51:02
Found 1 jplace file
Finished 2023-05-15 19:51:02 "
System information
Nextflow version: version 23.04.1 build 5866 Hardware: HPC Executor: local Container engine: conda OS: CentOS Linux Version of nf-core/ampliseq : 2.5.0 PICRUSt2 version : 2.5.2 gappa version: 0.8.0