grbot/16s-int-bt

16S Intermediate Bioinformatics training manuals

16s-int-bt's Issues

Error in validobject

Been testing the pipeline on our hpc and got the error

executor > local (12)
[a0/9eb871] process > runFastQC (rFQC.Dog1) [100%] 1 of 1 ✔
[d5/ac8150] process > runMultiQC (runMultiQC) [100%] 1 of 1 ✔
[ca/4cc6e6] process > filterAndTrim (16s_Dog1) [100%] 1 of 1 ✔
[2f/c29ece] process > runFastQC_postfilterandtrim... [100%] 1 of 1 ✔
[- ] process > runMultiQC_postfilterandtrim -
[06/1d1beb] process > mergeTrimmedTable (mergeTri... [100%] 1 of 1 ✔
[b1/9d6467] process > LearnErrorsFor (LearnErrors... [100%] 1 of 1 ✔
[3e/f5c57e] process > LearnErrorsRev (LearnErrors... [100%] 1 of 1 ✔
[58/dde33c] process > PoolSamplesInferDerepAndMer... [100%] 1 of 1 ✔
[2a/086856] process > RemoveChimeras (RemoveChime... [100%] 1 of 1 ✔
[- ] process > AssignTaxSpeciesRDP (Assign... -
[77/a891fc] process > RenameASVs (RenameASVs) [100%] 2 of 2, failed: 2...
[- ] process > GenerateSeqTables -
[- ] process > GenerateTaxTables -
[- ] process > AlignReadsDECIPHER -
[- ] process > GenerateTreePhangorn -
[- ] process > RootTree -
[- ] process > BiomFile -
[- ] process > ReadTracking -

aa/d3ea78] NOTE: Process RenameASVs (RenameASVs) terminated with an error exit status (1) -- Execution is retried (1) WARN: Killing pending tasks (1)

Error executing process > 'RenameASVs (RenameASVs)'

Caused by: Process RenameASVs (RenameASVs) terminated with an error exit status (1)
Command executed:

`

• !/usr/bin/env Rscript

• library(dada2)

• library(ShortRead)

• library(digest)

• st.all <- readRDS("seqtab_final.RDS")

• seqs <- colnames(st.all)

• ids_study <- switch("ASV", simple=paste("ASV", 1:ncol(st.all), sep = ""),
  md5=sapply(colnames(st.all), digest, algo="md5"))

• colnames(st.all) <- ids_study

generate FASTA

seqs.dna <- ShortRead(sread = DNAStringSet(seqs), id = BStringSet(ids_study))

Write out fasta file.

writeFasta(seqs.dna, file = 'asvs.simple.fna')

Write modified data

saveRDS(st.all, "seqtab_final.simple.RDS")
saveRDS(data.frame(id = ids_study, seq = seqs), "readmap.RDS")

Command exit status:
1

Command output:
(empty)

Command error:

The following object is masked from ‘package:base’:

  expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

  strsplit

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

  Vignettes contain introductory material; view with
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

  anyMissing, rowMedians

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

  colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

  aperm, apply, rowsum

Error in validObject(.Object) :
invalid class “ShortRead” object: sread() and id() length mismatch: 287, 0
Calls: ShortRead ... .local -> new -> initialize -> initialize -> validObject
Execution halted

Work dir:
/home/admin/test/16S-rDNA-dada2-pipeline/work/77/a891fcc311a51185c37253e03d6a0a

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

R version 4.0.2
nextflow version 20.04.1.5335

packageVersion("dada2")
[1] ‘1.16.0’

packageVersion("ShortRead")
[1] ‘1.46.0’
@grbot

Vagrant / Vbox versions

Error on; vagrant up

==> default: Booting VM...
There was an error while executing VBoxManage, a CLI used by Vagrant
for controlling VirtualBox. The command and stderr is shown below.

Command: ["startvm", "158c1f7c-e25c-4394-b9f0-0cad3f1f5585", "--type", "headless"]

Stderr: VBoxManage: error: The virtual machine 'vm-singularity_default_1633631952080_44504' has terminated unexpectedly during startup with exit code 1 (0x1)
VBoxManage: error: Details: code NS_ERROR_FAILURE (0x80004005), component MachineWrap, interface IMachine