Hello,
I am trying to run nf-core scrnaseq pipeline and store the results on minio server using the command :
os.system('nextflow run nf-core/scrnaseq -profile docker --input s3://alignment/samplesheet.csv \
--fasta s3:/'+ path_gen+' \--gtf s3:/'+path_ant+ ' --protocol \
'+dict_args["selectedProtocol"]+' --aligner alevin --outdir '+outdir+' \
-config nextflow_scrnaseq.config -bg --skip_emptydrops --save_align_intermeds false ')
I am using the using the config file :
aws {
accessKey ='***'
secretKey = '***'
region = 'us-east-1'
client {
endpoint = "*"
s3PathStyleAccess = true
}
}
workDir = 's3://intermediates/work'
At the end I get the following error :
[ef/2b9315] NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (SRR6496011) [ 50%] 1 of 2, failed: 1
[- ] NFCORE_SCRNASEQ:SCRNASEQ:GUNZIP_FASTA [ 0%] 0 of 1
[- ] NFCORE_SCRNASEQ:SCRNASEQ:GUNZIP_GTF [ 0%] 0 of 1
[- ] NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER -
[- ] NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX -
[- ] NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_QUANT -
[- ] NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:ALEVINQC -
[- ] NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD -
[- ] NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION:CONCAT_H5AD -
[- ] NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION:ANNDATAR_CONVERT -
[- ] NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (SRR6496011)'
Caused by:
Local executor requires the use of POSIX compatible file system — offending path: s3://intermediates/work/ef/2b93156a305d7d89a579b715dbafc7
Do you know why I get this error and what I am doing wrong ?
Thank in advance.
Loïc