Fatal INPUT FILE error, no valid exon lines in the GTF file: genes.gtf when using --genome GRCh38

[ianyfchang]

Description of the bug

When running nf-core/circrna with --genome GRCh38, the error happended.
I checked the fasta.fa downloaded from AWS, the chromosome name is not what I expected. The top 10 chromosome names:

$ ~/circrna_test/work/b0/e5217e456114a3a1f67f633ddf2687$ grep ">" fasta.fa

chr1gi:568336023LN:248956422rl:ChromosomeM5:6aef897c3d6ff0c78aff06ac189178ddAS:GRCh38
chr2gi:568336022LN:242193529rl:ChromosomeM5:f98db672eb0993dcfdabafe2a882905cAS:GRCh38
chr3gi:568336021LN:198295559rl:ChromosomeM5:76635a41ea913a405ded820447d067b0AS:GRCh38
chr4gi:568336020LN:190214555rl:ChromosomeM5:3210fecf1eb92d5489da4346b3fddc6eAS:GRCh38
chr5gi:568336019LN:181538259rl:ChromosomeM5:a811b3dc9fe66af729dc0dddf7fa4f13AS:GRCh38hm:47309185-49591369
chr6gi:568336018LN:170805979rl:ChromosomeM5:5691468a67c7e7a7b5f2a3a683792c29AS:GRCh38
chr7gi:568336017LN:159345973rl:ChromosomeM5:cc044cc2256a1141212660fb07b6171eAS:GRCh38
chr8gi:568336016LN:145138636rl:ChromosomeM5:c67955b5f7815a9a1edfaa15893d3616AS:GRCh38
chr9gi:568336015LN:138394717rl:ChromosomeM5:6c198acf68b5af7b9d676dfdd531b5deAS:GRCh38
chr10gi:568336014LN:133797422rl:ChromosomeM5:c0eeee7acfdaf31b770a509bdaa6e51aAS:GRCh38

Command used and terminal output

Command used: nextflow run nf-core/circrna -r dev --input sample_sheet_for_circrna.csv --outdir circrna_output  -profile docker  --phenotype phenotype_for_circrna_diff_expr.csv --module 'circrna_discovery,mirna_prediction,differential_expression' --tool_filter 2 --tool 'ciriquant,circexplorer2,find_circ,circrna_finder,mapsplice,dcc,segemehl' --genome GRCh38

Terminal output:
ERROR ~ Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:PREPARE_GENOME:STAR_GENOMEGENERATE (fasta.fa)'

Caused by:
  Process `NFCORE_CIRCRNA:CIRCRNA:PREPARE_GENOME:STAR_GENOMEGENERATE (fasta.fa)` terminated with an error exit status (104)


Command executed:

  samtools faidx fasta.fa
  NUM_BASES=`gawk '{sum = sum + $2}END{if ((log(sum)/log(2))/2 - 1 > 14) {printf "%.0f", 14} else {printf "%.0f", (log(sum)/log(2))/2 - 1}}' fasta.fa.fai`
  
  mkdir star
  STAR \
      --runMode genomeGenerate \
      --genomeDir star/ \
      --genomeFastaFiles fasta.fa \
      --sjdbGTFfile genes.gtf \
      --runThreadN 24 \
      --genomeSAindexNbases $NUM_BASES \
      --limitGenomeGenerateRAM 154518822656 \
      --sjdbOverhang 100
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CIRCRNA:CIRCRNA:PREPARE_GENOME:STAR_GENOMEGENERATE":
      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:
  104

Command output:
        STAR --runMode genomeGenerate --genomeDir star/ --genomeFastaFiles fasta.fa --sjdbGTFfile genes.gtf --runThreadN 24 --genomeSAindexNbases 14 --limitGenomeGenerateRAM 154518822656 --sjdbOverhang 100
        STAR version: 2.7.10a   compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
  Jun 08 01:49:15 ..... started STAR run
  Jun 08 01:49:15 ... starting to generate Genome files
  Jun 08 01:49:53 ..... processing annotations GTF

Command error:
        STAR --runMode genomeGenerate --genomeDir star/ --genomeFastaFiles fasta.fa --sjdbGTFfile genes.gtf --runThreadN 24 --genomeSAindexNbases 14 --limitGenomeGenerateRAM 154518822656 --sjdbOverhang 100
        STAR version: 2.7.10a   compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
  Jun 08 01:49:15 ..... started STAR run
  Jun 08 01:49:15 ... starting to generate Genome files
  Jun 08 01:49:53 ..... processing annotations GTF
  
  Fatal INPUT FILE error, no valid exon lines in the GTF file: genes.gtf
  Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.
  
  Jun 08 01:49:57 ...... FATAL ERROR, exiting

Work dir:
  /home/ian/NGSDATA_FOR_NEXTFLOW/Dr.LaiCH_RNASeq/work/b0/e5217e456114a3a1f67f633ddf2687

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`


 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

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

Relevant files

No response

System information

Nextflow version : 24.04.2
Hardware: Linux desktop
Executor: local
Container engine: Docker
OS: centos 7
Version of nf-core/circrna: dev

[nictru]

Please consider downloading your own reference genome data as described here