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Macs2 Output #388

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kittyBS opened this issue May 8, 2024 · 0 comments
Open

Macs2 Output #388

kittyBS opened this issue May 8, 2024 · 0 comments
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@kittyBS
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kittyBS commented May 8, 2024

Description of the bug

Hello,
I am aware that there is an open issue (#336) regarding this matter, but I still wanted to update the problem. Despite trying the codes below, I am unable to obtain the outputs from MACS2. Additionally, using the -genome parameter results in the following error: 'taging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BOWTIE2:BOWTIE2_ALIGN (1)' Caused by: Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView -- Check '.nextflow.log' file for details -[nf-core/chipseq] Pipeline completed with errors- WARN: Killing running tasks (1)'. Can you help me with this?
Best regards

Command used and terminal output

nextflow run nf-core/chipseq --input samplesheet.csv --genome GRCh38 --aligner bowtie2 --outdir chipseq --fasta GRCh38.primary_assembly.genome.fa.gz --gtf gencode.v38.primary_assembly.annotation.gtf.gz --macs_gsize 2913022398 --broad --save_maca_pileup -profile docker

nextflow run nf-core/chipseq --input 
samplesheet.csv --aligner bowtie2 --outdir /
chipseq --fasta GRCh38.primary_assembly.genome.fa.gz --gtf gencode.v38.primary_assembly.annotation.gtf.gz --macs_gsize 2913022398 -profile docker

Relevant files

No response

System information

Version of nf-core/chipseq 2.0.0
Hardware HPC
Executor slurm

@kittyBS kittyBS added the bug Something isn't working label May 8, 2024
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