STAR, CIRIquant, DCC errors during pipeline run about circrna

[nictru]

STAR

I encountered this problem before, but had no time to fix it yet. The problem is that the iGenomes STAR index is not compatible with the STAR version used in the pipeline. A workaround is setting manually setting star = null, which prevents usage of iGenomes and thus forces the pipeline to build an own index. Opened #91 for this.

CIRIquant

This is most probably due to missing escape characters in nextflow scripts, will be fixed via #83

DCC

Could potentially also be fixed via #83

What can you do now?

I expect #83 to be merged into dev within the next days, if you want to try it faster, you can use the caching branch of the pipeline (nextflow run -r caching ...). Keep me posted, in case something is working better then. If the problems (especially with DCC) persist, you could also try to fix the scripts yourself and open a PR.

[MariekeVromman]

Hi, just letting you know I ran with the merged bug fix #83, and also got a similar DCC error.

ValueError: invalid literal for int() with base 10: '2"'

details:

-[nf-core/circrna] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:CIRCRNA_DISCOVERY:DCC (control_1)'

Caused by:
  Process `NFCORE_CIRCRNA:CIRCRNA:CIRCRNA_DISCOVERY:DCC (control_1)` terminated with an error exit status (1)

Command executed:

  sed -i 's/^chr//g' gencode.v44.chr_patch_hapl_scaff.annotation.gtf

  mkdir control_1 && mv control_1.Chimeric.out.junction control_1 && printf "control_1/control_1.Chimeric.out.junction" > samplesheet
  mkdir control_1_mate1 && mv control_1_mate1.Chimeric.out.junction control_1_mate1 && printf "control_1_mate1/control_1_mate1.Chimeric.out.junction" > mate1file
  mkdir control_1_mate2 && mv control_1_mate2.Chimeric.out.junction control_1_mate2 && printf "control_1_mate2/control_1_mate2.Chimeric.out.junction" > mate2file

  DCC @samplesheet -mt1 @mate1file -mt2 @mate2file -D -an gencode.v44.chr_patch_hapl_scaff.annotation.gtf -Pi -ss -F -M -Nr 1 1 -fg -A GRCh38.p14.genome.fa -N -T 12

  awk '{print $6}' CircCoordinates >> strand
  paste CircRNACount strand | tail -n +2 | awk -v OFS="\t" '{print $1,$2,$3,$5,$4}' >> control_1.txt

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CIRCRNA:CIRCRNA:CIRCRNA_DISCOVERY:DCC":
      dcc: $(DCC --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  Output folder ./ already exists, reusing
  DCC 0.5.0 started
  24 CPU cores available, using 12
  WARNING: non-stranded data, the strand of circRNAs guessed from the strand of host genes
  Please make sure that the read pairs have been mapped both, combined and on a per mate basis
  Collecting chimera information from mates-separate mapping
  Combining individual circRNA read counts
  Using files _tmp_DCC/tmp_circCount and _tmp_DCC/tmp_coordinates for filtering
  Filtering by read counts
  Remove ChrM
  Count CircSkip junctions
  started circRNA detection from file _tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G
  	=> separating duplicates [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  	=> locating small circRNAs [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  	=> locating circRNAs (unstranded mode) [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  	=> merging circRNAs [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  	=> sorting circRNAs (unstranded mode) [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  finished circRNA detection from file _tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G

Command error:
  Unable to find image 'quay.io/biocontainers/circtools:1.2.1--pyh7cba7a3_0' locally
  1.2.1--pyh7cba7a3_0: Pulling from biocontainers/circtools
  73349e34840e: Already exists
  acab339ca1e8: Already exists
  425fd6205dc3: Pulling fs layer
  425fd6205dc3: Download complete
  425fd6205dc3: Pull complete
  Digest: sha256:7317627874031c4c9924d40b76602662a2d400c9ee4c1c626998c287e5e7bd65
  Status: Downloaded newer image for quay.io/biocontainers/circtools:1.2.1--pyh7cba7a3_0
  Output folder ./ already exists, reusing
  DCC 0.5.0 started
  24 CPU cores available, using 12
  Traceback (most recent call last):
    File "/usr/local/bin/DCC", line 10, in <module>
  WARNING: non-stranded data, the strand of circRNAs guessed from the strand of host genes
  Please make sure that the read pairs have been mapped both, combined and on a per mate basis
  Collecting chimera information from mates-separate mapping
  Combining individual circRNA read counts
  Using files _tmp_DCC/tmp_circCount and _tmp_DCC/tmp_coordinates for filtering
  Filtering by read counts
  Remove ChrM
  Count CircSkip junctions
      sys.exit(main())
    File "/usr/local/lib/python3.10/site-packages/DCC/main.py", line 490, in main
      CircSkipfiles = findCircSkipJunction(output_coordinates, options.tmp_dir,
    File "/usr/local/lib/python3.10/site-packages/DCC/main.py", line 679, in findCircSkipJunction
      circStartAdjacentExons, circStartAdjacentExonsIv = CCEM.findcircAdjacent(circStartExons, Custom_exon_id2Iv,
    File "/usr/local/lib/python3.10/site-packages/DCC/Circ_nonCirc_Exon_Match.py", line 281, in findcircAdjacent
      interval = Custom_exon_id2Iv[self.getAdjacent(ids, start=start)]
    File "/usr/local/lib/python3.10/site-packages/DCC/Circ_nonCirc_Exon_Match.py", line 222, in getAdjacent
      exon_number = int(custom_exon_id.split(':')[1]) - 1
  ValueError: invalid literal for int() with base 10: '2"'
  started circRNA detection from file _tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G
  	=> separating duplicates [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  	=> locating small circRNAs [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  	=> locating circRNAs (unstranded mode) [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  	=> merging circRNAs [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  	=> sorting circRNAs (unstranded mode) [_tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G]
  finished circRNA detection from file _tmp_DCC/control_1.Chimeric.out.junction.4ZYC4G

Work dir:
  /Users/marieke/Documents/work/66/1152ceffd34d8324ab17adcbacdcf6