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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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QIIME2_TREE fails running '-profile test,singularity' [not reproducible yet, please report when encountering!] #421

Closed aspitaleri closed 2 years ago

aspitaleri commented 2 years ago

Description of the bug

I have download the ampliseq pipeline singularity as follow: nf-core download then I run

nextflow run nf-core/ampliseq -profile test,singularity --outdir test

but it fails with:

Command used and terminal output

nextflow run nf-core/ampliseq -profile test,singularity --outdir test

N E X T F L O W  ~  version 22.04.0
Launching `https://github.com/nf-core/ampliseq` [maniac_franklin] DSL2 - revision: 306ad5df8f [master]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/ampliseq v2.3.1
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : maniac_franklin
  containerEngine           : singularity
  launchDir                 : /beegfs/scratch/ric.cirillo/spitaleri.andrea/MICROBIOME
  workDir                   : /beegfs/scratch/ric.cirillo/spitaleri.andrea/MICROBIOME/work
  projectDir                : /home/spitaleri.andrea/.nextflow/assets/nf-core/ampliseq
  userName                  : spitaleri.andrea
  profile                   : test,singularity
  configFiles               : /home/spitaleri.andrea/.nextflow/assets/nf-core/ampliseq/nextflow.config

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

Other input/output options
  qiime_adonis_formula      : treatment1
  sbdiexport                : true
  outdir                    : test

Cutoffs
  dada_tax_agglom_max       : 4
  qiime_tax_agglom_max      : 4

Taxonomic database
  dada_ref_taxonomy         : rdp=18
  cut_dada_ref_taxonomy     : true
  qiime_ref_taxonomy        : greengenes85

Filtering
  min_frequency             : 10
  min_samples               : 2

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

Staging foreign file: https://data.qiime2.org/2021.8/tutorials/training-feature-classifiers/85_otu_taxonomy.txt
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/ampliseq] Pipeline completed with errors-

WARN: Probably everything is fine, but this is a reminder that `--trunclenf` was set automatically to 230 and `--trunclenr` to 229. If this doesnt seem reasonable, then please change `--trunc_qmin` (and `--trunc_rmin`), or set `--trunclenf` and `--trunclenr` directly.
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE` terminated with an error exit status (1)

Command executed:

  export XDG_CONFIG_HOME="${PWD}/HOME"

  qiime alignment mafft         --i-sequences filtered-sequences.qza         --o-alignment aligned-rep-seqs.qza         --p-n-threads 2
  qiime alignment mask         --i-alignment aligned-rep-seqs.qza         --o-masked-alignment masked-aligned-rep-seqs.qza
  qiime phylogeny fasttree         --i-alignment masked-aligned-rep-seqs.qza         --p-n-threads 2         --o-tree unrooted-tree.qza
  qiime phylogeny midpoint-root         --i-tree unrooted-tree.qza         --o-rooted-tree rooted-tree.qza
  qiime tools export --input-path rooted-tree.qza          --output-path phylogenetic_tree
  cp phylogenetic_tree/tree.nwk .

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE":
      qiime2: $( qiime --version | sed -e "s/q2cli version //g" | tr -d '`' | sed -e "s/Run qiime info for more version details.//g" )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
  Plugin error from alignment:

    Command '['mafft', '--preservecase', '--inputorder', '--thread', '2', '/tmp/qiime2-archive-_4s90aq8/89cabafe-bc73-4459-bef2-42a088d62cfb/data/dna-sequences.fasta']' returned non-zero exit status 1.

  Debug info has been saved to /tmp/qiime2-q2cli-err-yzpf7b7a.log

Work dir:
  /beegfs/scratch/ric.cirillo/spitaleri.andrea/MICROBIOME/work/af/704fd8b32f3f246ccd9ca516849c05

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Relevant files

No response

System information

nextflow version 22.04 singularity version 3.6.4-1.el7

d4straub commented 2 years ago

I was not able to reproduce the error when using NXF_VER=22.04.0 nextflow run nf-core/ampliseq -r 2.3.1 -profile test,cfc --outdir test on our hpc where profile cfc can be found here.

aspitaleri commented 2 years ago

Hi running as suggested nextflow run nf-core/ampliseq -r 2.3.1 -profile test,singularity --outdir test -c ignore.config with ignore.config containing process { errorStrategy = 'ignore' }

I get this at the end

[dc/d0ce0a] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1a) [100%] 4 of 4 ✔ [2f/5c03eb] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (sampleID_2a) [100%] 4 of 4 ✔ [79/a3e486] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (sampleID_1a) [100%] 4 of 4 ✔ [62/d58600] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY (cutadapt_standard) [100%] 1 of 1 ✔ [76/981d9d] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE (cutadapt_standard_summary.tsv) [100%] 1 of 1 ✔ [17/f2dd40] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_QUALITY (FW) [100%] 2 of 2 ✔ [8e/f200b1] process > NFCORE_AMPLISEQ:AMPLISEQ:TRUNCLEN (RV) [100%] 2 of 2 ✔ [6f/3f5623] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_FILTNTRIM (sampleID_1) [100%] 4 of 4 ✔ [07/dd4fb8] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR (1) [100%] 1 of 1 ✔ [27/fa8b83] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING (1) [100%] 1 of 1 ✔ [33/4e256d] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA (1) [100%] 1 of 1 ✔ [8a/fd0cc7] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS (1) [100%] 1 of 1 ✔ [b0/0e5431] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE [100%] 1 of 1 ✔ [86/ee94f6] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS (1) [100%] 1 of 1 ✔ [59/fe4667] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP (ASV_seqs.fasta) [100%] 1 of 1 ✔ [a6/5cb37c] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY [100%] 1 of 1 ✔ [fc/8d0f58] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY (assignTaxonomy) [100%] 1 of 1 ✔ [d3/c440ab] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY (ASV_seqs.fasta,assignTaxonomy.trim.fastq.gz) [100%] 1 of 1 ✔ [24/21d2bb] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES (ASV_tax.rds,addSpecies.fna.gz) [100%] 1 of 1 ✔ [5a/092037] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME [100%] 1 of 1 ✔ [04/f39a40] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT (GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT) [100%] 1 of 1 ✔ [88/c813c8] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN (GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT) [100%] 1 of 1 ✔ [33/2c3b04] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ (ASV_seqs.fasta) [100%] 1 of 1 ✔ [2a/ab0b42] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY (rep-seqs.qza,GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-classifier.qza) [100%] 1 of 1 ✔ [72/3dd436] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV (ASV_table.tsv) [100%] 1 of 1 ✔ [11/632921] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ (ASV_seqs.fasta) [100%] 1 of 1 ✔ [ac/db4eaf] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX (ASV_tax_species.tsv) [100%] 1 of 1 ✔ [19/44ca36] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA (taxa:mitochondria,chloroplast;min-freq:10;min-samples:2) [100%] 1 of 1 ✔ [1c/330ed7] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS [100%] 1 of 1 ✔ [a5/c08988] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA (1) [100%] 1 of 1 ✔ [3e/3bcfe1] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE [100%] 1 of 1 ✔ [a7/663317] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV [100%] 1 of 1 ✔ [fd/c40186] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX [100%] 1 of 1 ✔ [82/1de47a] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2 (1) [100%] 1 of 1 ✔ [be/4a1071] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2 [100%] 1 of 1 ✔ [4c/fdc7e7] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT (1) [100%] 1 of 1 ✔ [62/2996e4] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) [100%] 1 of 1 ✔ [f7/ccb09c] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE (Metadata.tsv) [100%] 1 of 1 ✔ [a5/e08cea] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE [100%] 1 of 1, failed: 1 ✔ [- ] 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 - [9e/77e9ec] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERASV (treatment1,mix8,badpairwise10) [100%] 1 of 1 ✔ [d1/925e87] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_TAX (badpairwise10 - taxonomic level: 4) [100%] 9 of 9 ✔ [44/ddae20] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_ASV (badpairwise10) [100%] 3 of 3 ✔ [0a/b90385] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORT (ASV_table.tsv,ASV_tax_species.tsv,Metadata.tsv) [100%] 1 of 1 ✔ [b3/353c8e] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORTREANNOTATE (ASV_tax_species.tsv) [100%] 1 of 1 ✔ [c8/6734c7] process > NFCORE_AMPLISEQ:AMPLISEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1) [100%] 1 of 1 ✔ [b6/87f25c] process > NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC [100%] 1 of 1 ✔ -[nf-core/ampliseq] Pipeline completed successfully, but with errored process(es) - WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

Completed at: 28-Apr-2022 11:37:13 Duration : 4m 54s CPU hours : 0.3 (1.1% failed) Succeeded : 69 Ignored : 1 Failed : 1

d4straub commented 2 years ago

Problem:

[a5/e08cea] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE [100%] 1 of 1, failed: 1

I have used v2.3.1 now on multiple data sets and I havent had any trouble like this. As long as I cannot reproduce this I cannot fix it.

d4straub commented 2 years ago

Since there is no other report of that problem, I have to assume its on your end. If anyone comes across that issue again, please report it.