gappa Command error ?

[linshizuowei]

Hi, when I use gappa in picrust2, seems like thers is an error from gappa, error info described as below: " 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 "

It seems that there is no detailed error message，Is this an error about gappa ? please help me，thanks very much!

[lczech]

Hi @linshizuowei,

the gappa command used there seems to finish properly, my guess is hence that this is an issue in PyCrust. If so, please ask there for support - not much I can do if the issue is coming from there.

To confirm that gappa finished successfully, you can check that the output file of the gappa command is there. It should be /tmp/tmp8uspczvl/epa_out/epa_result_parsed.newick. This is a temporary path though, so it might be deleted shortly after running PyCrust. Did you specify that tmp directory, or is that something that PyCrust or your NextFlow setup are doing on their own? Maybe you can try to use a different directory for that (not /tmp), in order to make sure that intermediate files are kept for you to inspect.

Either way, try running it again, and check if the epa_result_parsed.newick exists ;-) If so, then gappa ran successfully, and the problem is with PyCrust or NextFlow. If not, can you please share the input file of gappa with me (/tmp/tmp8uspczvl/epa_out/epa_result_parsed.jplace - which is also in /tmp, and hence might also only be there shortly after running)?

Cheers Lucas

[linshizuowei]

Hi @lczech.

Thanks for your reply, I'll check the intermediate files to confirm if it's a gappa issue, and I'll also further confirm if it's a PyCrust issue. Thanks again for your answer.

Cheers

[lczech]

Hi @linshizuowei, any update on this issue?

[lczech]

Hey @linshizuowei, closing this issue for now, but feel free to re-open if you have an update :-)