Macs2 Output

[kittyBS]

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

[JoseEspinosa]

See the answer here regarding the macs issue.
Concerning the aws download problem, you can bypass the issue by manually downloading the iGenomes reference file and providing it to the pipeline using the --bowtie2_index parameter.
If you don't want to pre-download the file, from slacks exchanges this error is many times caused due to not be using a suitable java version, so you can also try to update java (Nextflow needs java 11 or later)

[JoseEspinosa]

I will close this issue now for lack of activity, if you have any further questions please feel free to re-open it.