souporcell_pipeline.py: command not found

[bednarsky]

Hi again! Sorry if I cause a lot of errors, really appreciate all your help!

Caused by: Process HADGE:run_multi:gene_demultiplexing:demultiplex_souporcell:souporcell (sampleID) terminated with an error exit status (127)

Command executed:

     mkdir souporcell_sampleID
     mkdir souporcell_sampleID/souporcell_out
     touch souporcell_sampleID/params.csv
     echo -e "Argument,Value

bamfile,sampleID__filtered_bam_file.bam barcode,barcodes.tsv.gz fasta,genome.fa threads,5 clusters,2 ploidy,2 min_alt,10 min_ref,10 max_loci,2048 restarts,None common_variant,No common variants are given. known_genotype,/path/to/project/results/demultiplexing/split_wgs_vcf/project.sampleID.vcf known_genotype_sample,No known sample names are given. skip_remap,True ignore,False " >> souporcell_sampleID/params.csv

     souporcell_pipeline.py --threads 32 -i sampleID__filtered_bam_file.bam -b barcodes.tsv.gz -f genome.fa -t 5 -k 2 --ploidy 2 --min_alt 10 --min_ref 10 --max_loci 2048               --known_genotypes unzipped.vcf  --skip_remap True  -o souporcell_sampleID/souporcell_out

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 26: souporcell_pipeline.py: command not found

Could this be due to the corrupted singularity image (https://github.com/theislab/hadge/issues/49)? I am cleaning my cache now and trying again

[wxicu]

How did you call the pipeline? Use which profile then?

[bednarsky]

How did you call the pipeline? Use which profile then?

I use the flag -profile cluster in my nextflow run .. call

Should I also put singularity.enabled = true into the cluster profile, then?

[wxicu]

How did you call the pipeline? Use which profile then?

I use the flag -profile cluster in my nextflow run .. call

Should I also put singularity.enabled = true into the cluster profile, then?

yes exactly, you can also do thay by using the existing profiles --profile cluster,conda_singularity. The second profile enables both conda and souporcell (check the latest doc, e.g. section "Quick start")

[bednarsky]

Ah sorry, overlooked that. Will try! Thanks for the quick help, really appreciate it!

[bednarsky]

Worked, thanks!