EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a

[petemeng]

Description of the bug

Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnasplice] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN (ERR204916)'

Caused by:
  Process `NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN (ERR204916)` terminated with an error exit status (105)

Command executed:

  STAR \
      --genomeDir STARIndex \
      --readFilesIn input1/ERR204916_1_val_1.fq.gz input2/ERR204916_2_val_2.fq.gz \
      --runThreadN 12 \
      --outFileNamePrefix ERR204916. \
       \
      --sjdbGTFfile genes_chrX.gtf \
      --outSAMattrRGline 'ID:ERR204916'  'SM:ERR204916'  \
      --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD--quantTranscriptomeBan Singleend



  if [ -f ERR204916.Unmapped.out.mate1 ]; then
      mv ERR204916.Unmapped.out.mate1 ERR204916.unmapped_1.fastq
      gzip ERR204916.unmapped_1.fastq
  fi
  if [ -f ERR204916.Unmapped.out.mate2 ]; then
      mv ERR204916.Unmapped.out.mate2 ERR204916.unmapped_2.fastq
      gzip ERR204916.unmapped_2.fastq
  fi

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN":
      star: $(STAR --version | sed -e "s/STAR_//g")
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
      gawk: $(echo $(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*$//')
  END_VERSIONS

Command exit status:
  105

Command output:
  	STAR --genomeDir STARIndex --readFilesIn input1/ERR204916_1_val_1.fq.gz input2/ERR204916_2_val_2.fq.gz --runThreadN 12 --outFileNamePrefix ERR204916. --sjdbGTFfile genes_chrX.gtf --outSAMattrRGline ID:ERR204916 SM:ERR204916 --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributesNH HI AS NM MD --quantTranscriptomeBan Singleend
  	STAR version: 2.7.9a   compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
  Jan 17 03:25:16 ..... started STAR run
  Jan 17 03:25:16 ..... loading genome

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  	STAR --genomeDir STARIndex --readFilesIn input1/ERR204916_1_val_1.fq.gz input2/ERR204916_2_val_2.fq.gz --runThreadN 12 --outFileNamePrefix ERR204916. --sjdbGTFfile genes_chrX.gtf --outSAMattrRGline ID:ERR204916 SM:ERR204916 --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributesNH HI AS NM MD --quantTranscriptomeBan Singleend
  	STAR version: 2.7.9a   compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
  Jan 17 03:25:16 ..... started STAR run
  Jan 17 03:25:16 ..... loading genome

  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

  Jan 17 03:25:16 ...... FATAL ERROR, exiting

Work dir:
  /ceph_disk3/mengpf/work/Project/Nextflow/rnasplice/work/5b/2c86f21fb9af7fc6b71f96eac9a670

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

 -- Check '.nextflow.log' file for details

Command used and terminal output

nextflow run rnasplice/main.nf \
--input samplesheet.csv \
--contrasts contrastsheet.csv    \
--genome GRCh37    \
--outdir result \
-profile docker \
--fasta /ceph_disk3/mengpf/work/Project/Nextflow/rnasplice/data/ref/X.fa.gz \
--gtf /ceph_disk3/mengpf/work/Project/Nextflow/rnasplice/data/ref/genes_chrX.gtf  \
--star_index /ceph_disk3/mengpf/work/Project/Nextflow/rnasplice/data/ref/STARIndex/

Relevant files

No response

System information

No response

[petemeng]

STARindex is download from s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/

[jma1991]

The problem is to with the pipeline, but with the STAR index version available through iGenomes. A similar issue has been documented within the rnavar pipeline, as detailed here. To address this, I recommend obtaining the FASTA/GFF files directly from iGenomes and supplying them to the pipeline. This approach would allow the pipeline to generate a compatible STAR index.