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ERROR ~ Error executing process > #823

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ohan-Bioinfo opened this issue Jan 10, 2025 · 4 comments
Open

ERROR ~ Error executing process > #823

ohan-Bioinfo opened this issue Jan 10, 2025 · 4 comments

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@ohan-Bioinfo
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[```
6d/5ee2aa] NFC…E_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_2) | 4 of 4 ✔
[3d/e651db] NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (sampleID_1) | 2 of 2
[bc/04cf26] NFC…MPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (sampleID_1a) | 2 of 2, failed: 2
[- ] NFC…PLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD -
[- ] NFC…ISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE -
[- ] NFC…E_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN -
[- ] NFC…_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM -
[- ] NFC…E_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY -
[- ] NFC…_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY -
[- ] NFC…E_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_ADDSPECIES -
[- ] NFC…AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_INTAX_QIIME2 -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TABLEFILTERTAXA -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA -
[- ] NFC…AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE -
[- ] NFC…E_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV -
[- ] NFC…E_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX -
[- ] NFC…E_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2 -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2 -
[- ] NFC…E_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_PPLACE -
[- ] NFC…E_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_SINTAX -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT -
[- ] NFC…AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG -
[- ] NFC…Q:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG -
[50/a80f88] NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) | 1 of 1 ✔
[af/bdfacb] NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE (Metadata.tsv) | 1 of 1 ✔
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE -
[- ] NFC…ISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION -
[- ] NFC…PLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_CORE -
[- ] NFC…LISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ALPHA -
[- ] NFC…PLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETA -
[- ] NFC…ISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ADONIS -
[- ] NFC…SEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETAORD -
[- ] NFC…LISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_ASV -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:ANCOMBC_FORMULA_TAX -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:ANCOMBC_FORMULA_ASV -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORT -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORTREANNOTATE -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ_INASV -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT -
Use DADA2 taxonomy classification
Execution cancelled -- Finishing pending tasks before exit
Staging foreign file: https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otus.fasta
Staging foreign file: https://data.gtdb.ecogenomic.org/releases/release207/207.0/genomic_files_reps/bac120_ssu_reps_r207.tar.gz
Staging foreign file: https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otu_taxonomy.txt
Staging foreign file: https://data.gtdb.ecogenomic.org/releases/release207/207.0/genomic_files_reps/ar53_ssu_reps_r207.tar.gz
-[nf-core/ampliseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (sampleID_1)'

Caused by:
Process NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (sampleID_1) terminated with an error exit status (127)

Command executed:

cutadapt
-Z
--cores 4
--minimum-length 1 -O 3 -e 0.1 -g GTGYCAGCMGCCGCGGTAA -G GGACTACNVGGGTWTCTAAT --discard-untrimmed
-o sampleID_1.trimmed_1.trim.fastq.gz -p sampleID_1.trimmed_2.trim.fastq.gz
sampleID_1_1.fastq.gz sampleID_1_2.fastq.gz
> sampleID_1.trimmed.cutadapt.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC":
cutadapt: $(cutadapt --version)
END_VERSIONS

Command exit status:
127

Command output:
(empty)

Command error:
.command.sh: line 9: cutadapt: command not found

Work dir:
/home/emz/Storage/Data/Lama-16S-ITs/Nfcore-ampliseq/work/76/3b6998f859dc2579eb6d5c276049c6

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- 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
WARN: [NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY] Unable to resume cached task -- See log file for details
Waiting for file transfers to complete (1 files)


Please advice i have been running the pipeline but reach alwys a leve and keep silent without running.

Now i attempt to run test profile is there anything that i can do to make this pipeline works?
@ohan-Bioinfo
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Errors here alwys

J```
an-10 18:54:20.273 [main] DEBUG nextflow.Session - Session await
Jan-10 18:54:20.280 [Actor Thread 81] DEBUG nextflow.splitter.AbstractSplitter - Creating gzip splitter for: /home/emz/Storage/Data/Lama-16S-ITs/140/Raw/100.fq.gz
Jan-10 18:54:20.378 [Actor Thread 68] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.016 s; total time: 0.018 s
Jan-10 18:54:20.378 [Actor Thread 66] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.016 s; total time: 0.018 s
Jan-10 18:54:20.383 [Actor Thread 68] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/emz/Storage/Data/Lama-16S-ITs/Nfcore-ampliseq/work/collect-file/a12e1cd37798fadcd9090ffc73287c8c
Jan-10 18:54:20.383 [Actor Thread 66] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/emz/Storage/Data/Lama-16S-ITs/Nfcore-ampliseq/work/collect-file/de6032e8d26ca00e1bb1b2cb56d06d61
Jan-10 18:54:20.392 [Actor Thread 68] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-6381097615419958645
Jan-10 18:54:20.392 [Actor Thread 66] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-7990858929242876234
Jan-10 18:54:21.610 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240904.tar.gz to work dir: /home/emz/Storage/Data/Lama-16S-ITs/Nfcore-ampliseq/work/stage-cf75ce98-91c6-4dbd-b9ee-bbd664a43b77/79/88e8f390cc133900263feb765b7b66/k2_standard_20240904.tar.gz
Jan-10 18:54:23.611 [Actor Thread 66] INFO nextflow.file.FilePorter - Staging foreign file: https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240904.tar.gz
Jan-10 18:54:30.199 [Actor Thread 81] DEBUG nextflow.splitter.AbstractSplitter - Creating gzip splitter for: /home/emz/Storage/Data/Lama-16S-ITs/140/Raw/101.fq.gz
Jan-10 18:54:30.375 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:54:30.379 [Task submitter] INFO nextflow.Session - [10/73968f] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (S100)
Jan-10 18:54:31.450 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (S100); status: COMPLETED; exit: 0; error: -; workDir: /home/emz/Storage/Data/Lama-16S-ITs/Nfcore-ampliseq/work/10/73968fb716bc62a9d3bd36c32d0c2c]
Jan-10 18:54:31.452 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=264; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-10 18:54:31.545 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:54:31.547 [Task submitter] INFO nextflow.Session - [7d/fc8f92] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (S100)
Jan-10 18:54:41.047 [Actor Thread 81] DEBUG nextflow.splitter.AbstractSplitter - Creating gzip splitter for: /home/emz/Storage/Data/Lama-16S-ITs/140/Raw/102.fq.gz
Jan-10 18:54:41.078 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:54:41.079 [Task submitter] INFO nextflow.Session - [3e/193345] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (S101)
Jan-10 18:54:41.981 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (S101); status: COMPLETED; exit: 0; error: -; workDir: /home/emz/Storage/Data/Lama-16S-ITs/Nfcore-ampliseq/work/3e/1933455df55b70686902eedecf2486]
Jan-10 18:54:42.008 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:54:42.009 [Task submitter] INFO nextflow.Session - [a4/730977] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (S101)
Jan-10 18:54:52.123 [Actor Thread 81] DEBUG nextflow.splitter.AbstractSplitter - Creating gzip splitter for: /home/emz/Storage/Data/Lama-16S-ITs/140/Raw/103.fq.gz
Jan-10 18:54:52.146 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:54:52.147 [Task submitter] INFO nextflow.Session - [48/19b21c] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (S102)
Jan-10 18:54:53.147 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (S102); status: COMPLETED; exit: 0; error: -; workDir: /home/emz/Storage/Data/Lama-16S-ITs/Nfcore-ampliseq/work/48/19b21cef5ae380527afc5039608580]
Jan-10 18:54:53.176 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:54:53.177 [Task submitter] INFO nextflow.Session - [a0/3871b6] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (S102)
Jan-10 18:55:00.546 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:55:00.547 [Task submitter] INFO nextflow.Session - [eb/762575] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (S103)
Jan-10 18:55:02.290 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (S103); status: COMPLETED; exit: 0; error: -; workDir: /home/emz/Storage/Data/Lama-16S-ITs/Nfcore-ampliseq/work/eb/76257585a7fae7faeccae3247f6862]
Jan-10 18:55:02.320 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:55:02.321 [Task submitter] INFO nextflow.Session - [78/a7c7dd] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (S103)
Jan-10 18:55:02.339 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-10 18:55:02.340 [Task submitter] INFO nextflow.Session - [fd/1639a5] Submitted process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 (single_end)

@d4straub
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Hi there,
thanks for copying the error message.
However, its as well important how you started the pipeline. Please copy paste here the exact command that you used to run the pipeline and used config files, if any.

@ohan-Bioinfo
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Here is how i started
nextflow run nf-core/ampliseq --input samplesheet_fixed.tsv --outdir results --single_end --kraken2_ref_taxonomy standard --skip_fastqc --metadata metadata_fixed.tsv -profile docker -r 2.12.0 --skip_cutadapt

@d4straub
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Hi there,
with that command you should not be able to get that output. Can you run the test profile to make sure its not your data and your setup is fine? Use nextflow run nf-core/ampliseq -r 2.12.0 -profile test,docker --outdir results_test

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@ohan-Bioinfo @d4straub