ERROR nextflow.cli.Launcher

[quynhbui1907]

Bonjour,
J'ai eu un message d'erreur si dessous en utilisant le pipeline pacvar sur mes données PacBioHiFi.
Pourriez vous m'aider svp?
Je vous remercie d'avance.
Bien cordialement,
Quynh BUI

.nextflow.log

.nextflow.log

---

Feb-13 11:03:06.803 [main] ERROR nextflow.cli.Launcher - Argument of file func
on cannot be null
java.lang.IllegalArgumentException: Argument of file function cannot be null
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface
ava:321)

[elementnumber50]

I had this error too.

I associated it to the first demultiplexing step. You need to assign demultiplexing as false

--skip_demultiplexing

I did not need to demultiplex. If you need to demultiplex, you probably need a barcodes file.

[quynhbui1907]

@elementnumber50 : Thank you so much, I'll try with the option --skip_demultiplexing
Have a nice day!

[quynhbui1907]

Hi @elementnumber50 It still didn't work. Could you help me please?
Here is the parameters I used:
"input": "/shared/projects/pancherry/pacvar/samplesheetlong_tests.csv",
"outdir": "/shared/projects/pancherry/pacvar/results",
"email": "quynh-trang.bui@inrae.fr",
"multiqc_title": "pacvar_cherry",
"genome": null,
"fasta": "/shared/projects/pancherry/ref/Prunus_avium_TietonV2.chr.fasta",
"fasta_fai": "/shared/projects/pancherry/ref/Prunus_avium_TietonV2.chr.fasta.fai",
"dict": "/shared/projects/pancherry/ref/Prunus_avium_TietonV2.chr.dict",
"workflow": "wgs",
"snv_caller": "gatk4",
"skip_demultiplexing": true

And please find in attachement the log file and samplesheet.

samplesheetlong_tests.csv
.nextflow.log