ampliseq
ampliseq copied to clipboard
nf-core
ERROR: R_HOME ('/usr/local/lib/R') not found
Description of the bug
I installed nextflow using conda.
R is installed in conda.
(env_nf) [train@localhost ampliseq]$ which R
~/mambaforge/envs/env_nf/bin/R
I used this command: nextflow run nf-core/ampliseq -profile test,docker --outdir test -resume -with-conda
I got this error. How can I fix it?
Execution cancelled -- Finishing pending tasks before exit -[nf-core/ampliseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv)'
Caused by:
Process NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) terminated with an error exit status (1)
Command executed:
metadata_all.r Metadata.tsv
cat <<-END_VERSIONS > versions.yml "NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL": R: $(R --version 2>&1 | sed -n 1p | sed 's/R version //' | sed 's/ (.*//') END_VERSIONS
Command exit status: 1
Command output: (empty)
Command error: ERROR: R_HOME ('/usr/local/lib/R') not found
Work dir: /home/train/80-1372045246/ampliseq/work/41/fe8be8d5b86f25bb8d93905895f87c
Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
-- Check '.nextflow.log' file for details
Command used and terminal output
No response
Relevant files
No response
System information
No response
Try without the -with-conda. Since you're running with -profile docker, Nextflow will use Docker for software, so I imagine the -with-conda flag might confuse.
Next time, for quicker responses, post at the nf-core Slack #ampliseq channel. Join here: https://nf-co.re/join/slack (there might be some problems with joining now, try later if there is).
Thank you for your reply. Using commond: nextflow run nf-core/ampliseq -profile test,docker --outdir test -resume, still generate this error.
(env_nf) [train@localhost ampliseq]$ nextflow run nf-core/ampliseq -profile test,docker --outdir ampliseq-test -resume
N E X T F L O W ~ version 23.10.1
Launching https://github.com/nf-core/ampliseq [crazy_watson] DSL2 - revision: 717abb8a03 [master]
WARN: No DADA2 cutoffs were specified (--trunclenf & --trunclenr), therefore reads will be truncated where median quality drops below 25 (defined by --trunc_qmin) but at least a fraction of 0.75 (defined by --trunc_rmin) of the reads will be retained.
The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.
WARN: Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
nf-core/ampliseq v2.9.0-g717abb8
Core Nextflow options revision : master runName : crazy_watson containerEngine : docker launchDir : /home/train/80-1372045246/ampliseq workDir : /home/train/80-1372045246/ampliseq/work projectDir : /home/train/.nextflow/assets/nf-core/ampliseq userName : train profile : test,docker configFiles :
Main arguments input : https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet.tsv FW_primer : GTGYCAGCMGCCGCGGTAA RV_primer : GGACTACNVGGGTWTCTAAT metadata : https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Metadata.tsv outdir : ampliseq-test
ASV post processing vsearch_cluster : true filter_ssu : bac max_len_asv : 255
Taxonomic database dada_ref_taxonomy : gtdb=R07-RS207 cut_dada_ref_taxonomy : true qiime_ref_taxonomy : greengenes85
ASV filtering min_frequency : 10 min_samples : 2
Downstream analysis metadata_category_barplot : treatment1,badpairwise10 qiime_adonis_formula : treatment1,mix8 sbdiexport : true tax_agglom_max : 4
Max job request options max_cpus : 2 max_memory : 6.GB max_time : 6.h
Institutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function
!! Only displaying parameters that differ from the pipeline defaults !!
If you use nf-core/ampliseq for your analysis please cite:
-
The pipeline 10.5281/zenodo.1493841
-
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
-
Software dependencies https://github.com/nf-core/ampliseq/blob/master/CITATIONS.md
[- ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY - executor > local (2) [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY - executor > local (2) [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_ADDSPECIES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_INTAX_QIIME2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TABLEFILTERTAXA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_PPLACE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_SINTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG - [f1/e1db85] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) [ 0%] 0 of 1 [db/a23d4a] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE (Metadata.tsv) [ 0%] 0 of 1 [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION - executor > local (2) [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_ADDSPECIES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_INTAX_QIIME2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TABLEFILTERTAXA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_PPLACE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_SINTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG - [f1/e1db85] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) [100%] 1 of 1, failed: 1 ✘ [db/a23d4a] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE (Metadata.tsv) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_CORE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ALPHA - executor > local (2) [f1/1c7b20] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1) [ 75%] 3 of 4, cached: 3 [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY [ 0%] 0 of 1 [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_ADDSPECIES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME [ 0%] 0 of 1 [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_INTAX_QIIME2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TABLEFILTERTAXA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_PPLACE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_SINTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG - [f1/e1db85] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) [100%] 1 of 1, failed: 1 ✘ [db/a23d4a] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE (Metadata.tsv) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_CORE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ALPHA - executor > local (2) [f1/1c7b20] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1) [ 75%] 3 of 4, cached: 3 [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY [ 0%] 0 of 1 [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_ADDSPECIES - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME [ 0%] 0 of 1 [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_INTAX_QIIME2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TABLEFILTERTAXA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2 - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_PPLACE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_SINTAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG - [f1/e1db85] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) [100%] 1 of 1, failed: 1 ✘ [db/a23d4a] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE (Metadata.tsv) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_CORE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ALPHA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETA - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ADONIS - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETAORD - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_TAX - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_ASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORT - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORTREANNOTATE - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ_INASV - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC - [- ] process > NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT - Use DADA2 taxonomy classification Execution cancelled -- Finishing pending tasks before exit -[nf-core/ampliseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv)'
Caused by:
Process NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) terminated with an error exit status (1)
Command executed:
metadata_all.r Metadata.tsv
cat <<-END_VERSIONS > versions.yml "NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL": R: $(R --version 2>&1 | sed -n 1p | sed 's/R version //' | sed 's/ (.*//') END_VERSIONS
Command exit status: 1
Command output: (empty)
Command error: ERROR: R_HOME ('/usr/local/lib/R') not found
Work dir: /home/train/80-1372045246/ampliseq/work/f1/e1db8575d09b3b06292bb234d455a6
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
-- Check '.nextflow.log' file for details
Try installing Nextflow natively instead of in a Conda environment, i.e. deactivate the Conda environment and follow the instructions here: https://www.nextflow.io/ (under "Getting started").
@WangLab-SCSIO did that or any other procedure resolve your problem? If yes, please give feedback and close the issue. If not, please also let us know.
I close that issue now because of missing response. Feel free to open it again in case you continue to have the issue.