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nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
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STAR_ALIGN error "Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView" #94

Open BurtonChia opened 1 year ago

BurtonChia commented 1 year ago

Description of the bug

Running nf-core/rnavar:1.0.0 with genome references from igenome or user-specified fasta/gtf files will both encounter the following error when in the STAR_ALIGN stage:

"Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView"

Command used and terminal output

nextflow run nf-core/rnavar -r 1.0.0 \
--input /mnt/scratch/projects/adipocytes/samplesheet-bulkRNAseq-variant_calling.csv \
--outdir /mnt/scratch/projects/adipocytes/results/GRCh38-2023-A/rnaseq-variant_calling \
--genome GRCh38 \
--known_indels /mnt/scratch/projects/adipocytes/popscle/filtervcf.minAF.freemuxlet.vcf.gz \
--save_reference \
--max_cpus 30 \
--max_memory 235GB \
-resume \
-profile singularity

executor >  local (5)
[-        ] process > NFCORE_RNAVAR:RNAVAR:PREPAR... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:PREPAR... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:PREPAR... -
[41/23e647] process > NFCORE_RNAVAR:RNAVAR:INPUT_... [100%] 1 of 1, cached: 1 ✔
[-        ] process > NFCORE_RNAVAR:RNAVAR:CAT_FASTQ -
[66/fea76f] process > NFCORE_RNAVAR:RNAVAR:FASTQC... [  0%] 0 of 15
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:MARKDU... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:SPLITN... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:SPLITN... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:SPLITN... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:TABIX     -
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:CUSTOM... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:MULTIQC   -
Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
Error executing process > 'NFCORE_RNAVAR:RNAVAR:ALIGN_STAR:STAR_ALIGN (A20S35242OM)'

Caused by:
  Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView

Relevant files

No response

System information

ankurs103 commented 1 year ago

Is it resolved? I am also facing the same error message "Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView"