Missing STAR index not created automaticaly

[kunstner]

Description of the bug

Hi,
I'm running rnavar v1.0.0 on GRCm38. Genomes and indices were downloaded using igenomes. I got troubles during the STAR alignment step. According to documentation, a new STAR index should automatically be created if the index version does not match the installed STAR version (#37 (comment)). However, this process does not start and the workflow ends with an error

Error executing process > 'NFCORE_RNAVAR:RNAVAR:ALIGN_STAR:STAR_ALIGN (s9)'

Any ideas how I can fix this quickly so that the index gets created on the fly?

Many thanks,
Axel

Command used and terminal output

nextflow run nf-core/rnavar -r 1.0.0 \
	-profile singularity \
	-resume \
	--igenomes_base ./references \
	--input samplesheet.csv --genome GRCm38 \
	--dbsnp references/Mus_musculus/Ensembl/GRCm38/Annotation/Variation/Mus_musculus.vcf.gz \
	--dbsnp_tbi references/Mus_musculus/Ensembl/GRCm38/Annotation/Variation/Mus_musculus.vcf.gz.tbi \
	--outdir ./results_single_end \
	--annotate_tools vep \
	--genome GRCm38 \
	--skip_variantannotation


Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnavar] Pipeline completed with errors-
Error executing process > 'NFCORE_RNAVAR:RNAVAR:ALIGN_STAR:STAR_ALIGN (s9)'

Caused by:
  Process `NFCORE_RNAVAR:RNAVAR:ALIGN_STAR:STAR_ALIGN (s9)` terminated with an error exit status (105)

Command executed:

  STAR \
      --genomeDir STARIndex \
      --readFilesIn GFI1_36S_S_MLL_AF9_3.fastq.gz  \
      --runThreadN 12 \
      --outFileNamePrefix s9. \
       \
      --sjdbGTFfile genes.gtf \
      --outSAMattrRGline ID:s9 'SM:s9' 'PL:illumina'  \
      --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat  --sjdbOverhang 149 --twopassMode Basic  --outBAMsortingBinsN 50 --limitOutSJcollapsed 1000000
  
  
  
  if [ -f s9.Unmapped.out.mate1 ]; then
      mv s9.Unmapped.out.mate1 s9.unmapped_1.fastq
      gzip s9.unmapped_1.fastq
  fi
  if [ -f s9.Unmapped.out.mate2 ]; then
      mv s9.Unmapped.out.mate2 s9.unmapped_2.fastq
      gzip s9.unmapped_2.fastq
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAVAR:RNAVAR:ALIGN_STAR:STAR_ALIGN":
      star: $(STAR --version | sed -e "s/STAR_//g")
  END_VERSIONS

Command exit status:
  105

Command output:
  	STAR --genomeDir STARIndex --readFilesIn GFI1_36S_S_MLL_AF9_3.fastq.gz --runThreadN 12 --outFileNamePrefix s9. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:s9 SM:s9 PL:illumina --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --sjdbOverhang 149 --twopassMode Basic --outBAMsortingBinsN 50 --limitOutSJcollapsed 1000000
  	STAR version: 2.7.9a   compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
  Aug 08 09:51:40 ..... started STAR run
  Aug 08 09:51:41 ..... loading genome

Command error:
  WARNING: Ignoring /data/sb_service_01/ak_20220805_SomaticSignatures_174 bind mount: user bind control disabled by system administrator
  WARNING: Ignoring /home/kuenstner/.nextflow/assets/nf-core/rnavar/bin bind mount: user bind control disabled by system administrator
  WARNING: Ignoring /data/sb_service_01/ak_20220805_SomaticSignatures_174/work/dc/0bc41c5077de6d940513d659ce71d4 bind mount: user bind control disabled by system administrator
  WARNING: Not mounting current directory: user bind control is disabled by system administrator
  
  EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a
  SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a
  
  Aug 08 09:51:41 ...... FATAL ERROR, exiting

Work dir:
  /data/sb_service_01/ak_20220805_SomaticSignatures_174/work/dc/0bc41c5077de6d940513d659ce71d4

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

No response

[praveenraj2018]

@kunstner Thanks for reporting this. We are aware of this and purposefully skipped it as there were some technical challenges while implementing this check. We will certainly take this into account in the next patch release.

[bounlu]

Hi @praveenraj2018

Has this been already fixed in the dev branch?

[lescai]

got the same problem here @praveenraj2018. is there a suggested way around while you manage to implement a fix?
maybe a star-indexed local reference?

[kunstner]

You can easily build the star index yourself. Just make sure you use the same version of STAR as RNAvar (e.g. STAR 2.7.9a).

The following command should do the job nicely:

STARINDEX=star_index
fasta=$REFERENCE_DIR/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa
gtf=$REFERENCE_DIR/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf

STAR --runMode genomeGenerate --genomeDir $STARINDEX --genomeFastaFiles $fasta --sjdbGTFfile $gtf --runThreadN 32

[WhoisDonlee]

The star parameter is still set in conf/igenomes.config, so the pipeline thinks a star index is provided.

Remove or comment the star = "${params.igenomes_base}... line, this will trigger the STAR_GENOMEGENERATE process to run.