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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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tuple index out of range error at ancom #153

Closed MonicaSteffi closed 3 years ago

MonicaSteffi commented 4 years ago

Dear all,

I am trying nf-core amplicon for 5 different multiple sequencing runs. It got the error at ancom-tax step. 


Error executing process > 'ancom_tax (Nature-level2)'

Caused by:
  Process `ancom_tax (Nature-level2)` terminated with an error exit status (1)

Command executed:

  qiime taxa collapse           --i-table Nature.qza            --i-taxonomy taxonomy.qza               --p-level 2             --o-collapsed-table lvl2-Nature.qza
  qiime composition add-pseudocount             --i-table lvl2-Nature.qza               --o-composition-table comp-lvl2-Nature.qza
  qiime composition ancom               --i-table comp-lvl2-Nature.qza          --m-metadata-file meta_data.tsv                 --m-metadata-column Nature           --o-visualization comp-lvl2-Nature.qzv
  qiime tools export --input-path comp-lvl2-Nature.qzv          --output-path ancom/Category-Nature-level-2

Command exit status:
  1

Command output:
  Saved FeatureTable[Frequency] to: lvl2-Nature.qza
  Saved FeatureTable[Composition] to: comp-lvl2-Nature.qza

Command error:
  Plugin error from composition:

    tuple index out of range

  Debug info has been saved to /tmp/qiime2-q2cli-err-z5bj_63u.log

My metadata as follows:

Sample-id | Nature
run1-252003XS-S118-L001  ORA2018
run1-252015XS-S164-L001  ORA2018
:
run2-2019-047-0001  FOCUS
run2-2019-047-0002  FOCUS
: 
run3-10032 ORA
run3-10043 ORA
: 
run4-001-S2-L001  enable
run4-002-S3-L001  enable
:
run5-326-S326-L001  S1-T4
run5-327-S327-L001  S1-T4
:
run5-first-01-D1  S1-T1
run5-first-02-D2  S1-T1
:
run5-second-01-10-00  S1-T2
run5-second-02-8-00  S1-T2
:
run5-third-06-t7-30  S1-T3
run5-third-07-t60  S1-T3

Is it problem with my meta data?

And I executed the following command

nextflow run nf-core/ampliseq -profile standard -c nextflow_standard.config --reads data --FW_primer TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG --RV_primer GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC --metadata meta_data.tsv --multipleSequencingRuns --trunclenf 232 --trunclenr 227 --keepIntermediates --min_frequency 0 --classifier ~/RDP/RDP_classifier_sub.qza

d4straub commented 4 years ago

Hi there, could you check the number of features at Taxonomic Level 2 in results/barplot/index.html? If its just 1 feature than this is the problem. By the way, it is good practice to use e.g. -r 1.1.2 to fix the pipeline version.

d4straub commented 3 years ago

I close that because of no reply.