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
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.configN E X T F L O W ~ version 21.10.6 LaunchingCalliNGS-NF/main.nf[pensive_kalman] - revision: d02d9193b8 C A L L I N G S - N F v 2.1genome : /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