invalid class “ShortRead” object: sread() and id() length mismatch

[grbot]

The Travis run fails because of an "invalid class “ShortRead” object: sread() and id() length mismatch" error in the RenameASVs process. See: https://travis-ci.com/github/h3abionet/16S-rDNA-dada2-pipeline . I ran the workflow manually and also run into the error.

The issue seems to be from the commit here: https://github.com/h3abionet/16S-rDNA-dada2-pipeline/commit/c3522427eb576f3d43652b37c71a8c19bf42962c#diff-28b7bea57b04f15beeb4c1de0ee78382L938 . As I understand it the switch was correctly setup before the change.

[cjfields]

@grbot I'll have a look.

[espirado]

@grbot just tested the pipeline and ran into the same issue any workaround ?

[cjfields]

@grbot @espirado is this using the standard test data or the full data set? I'm setting this up to test.

[grbot]

@cjfields both the standard test data and full data set is an issue.

[cjfields]

Yep, able to reproduce:

...
  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: 62, 0
  Calls: ShortRead ... .local -> new -> initialize -> initialize -> validObject
  Execution halted

Work dir:
  /home/groups/h3abionet/Microbiome-Tests/results/2020-09-26-issue10/work/34/88075171fb6daeaa01906b0bf40144

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Will see if II can work it out but may revert on master

[cjfields]

I've committed a small fix for this but read tracking at the end seems broken now (I think it's unrelated but will check).

[cjfields]

The ReadTracking error is a bit odd, locally this works fine. I'll post a separate issue from the error reported here but will link it just in case.

[cjfields]

@grbot I think this should work now (with the exception of single-sample case), but reopen if there are still issues on your end.