Could not build fai index genome.fa.fai
Jokendo-collab opened this issue · 0 comments
I am getting the below error when I try to run this pipeline on HPC with -profile singularity. Our HPC does not support docker. Could you help in solving this?
nextflow run CalliNGS-NF/ -profile singularity --genome /scratch/oknjav001/sarsCovRNA/CalliNGS-NF/data/genome.fa -c CalliNGS-NF/nextflow.config
N E X T F L O W ~ version 21.10.6
Launching CalliNGS-NF/main.nf [pensive_kalman] - revision: d02d9193b8
C A L L I N G S - N F v 2.1
genome : /scratch/oknjav001/sarsCovRNA/CalliNGS-NF/data/genome.fa
reads : /scratch/oknjav001/sarsCovRNA/CalliNGS-NF/data/reads/rep1_{1,2}.fq.gz
variants : /scratch/oknjav001/sarsCovRNA/CalliNGS-NF/data/known_variants.vcf.gz
denylist : /scratch/oknjav001/sarsCovRNA/CalliNGS-NF/data/denylist.bed
results : results
executor > local (4)
[77/d01b20] process > PREPARE_GENOME_SAMTOOLS (genome) [ 0%] 0 of 1
[72/3c89cf] process > PREPARE_GENOME_PICARD (genome) [ 0%] 0 of 1
[03/63ccdb] process > PREPARE_STAR_GENOME_INDEX (genome) [ 0%] 0 of 1
executor > local (4)
[77/d01b20] process > PREPARE_GENOME_SAMTOOLS (genome) [100%] 1 of 1, failed: 1 ✘
[- ] process > PREPARE_GENOME_PICARD (genome) -
[03/63ccdb] process > PREPARE_STAR_GENOME_INDEX (genome) [100%] 1 of 1, failed: 1 ✘
[66/5dbe33] process > PREPARE_VCF_FILE (known_variants.vcf) [100%] 1 of 1 ✔
[- ] process > RNASEQ_MAPPING_STAR -
[- ] process > RNASEQ_GATK_SPLITNCIGAR -
[- ] process > RNASEQ_GATK_RECALIBRATE -
[- ] process > RNASEQ_CALL_VARIANTS -
[- ] process > POST_PROCESS_VCF -
[- ] process > PREPARE_VCF_FOR_ASE -
[- ] process > ASE_KNOWNSNPS -
Error executing process > 'PREPARE_GENOME_SAMTOOLS (genome)'
Caused by:
Process PREPARE_GENOME_SAMTOOLS (genome) terminated with an error exit status (255)
Command executed:
samtools faidx genome.fa
Command exit status:
255
Command output:
(empty)
Command error:
[fai_build] fail to open the FASTA file genome.fa
Could not build fai index genome.fa.fai
Work dir:
/scratch/oknjav001/sarsCovRNA/work/77/d01b200797821f93eb4177ceaa3c77
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out