I am newbie to < C038XMTQWBT|> and I am having Argument of f nf-core #genomeassembler

I am newbie to <#C038XMTQWBT|> and I am having "Ar...

Sadik

04/03/2025, 5:01 PM

I am newbie to #C038XMTQWBT and I am having "Argument of file function cannot be null" and not sure how to deal with it. Any idea?

Apr-03 17:48:46.358 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination

Apr-03 17:48:46.358 [main] DEBUG nextflow.Session - Session await

Apr-03 17:48:46.436 [Actor Thread 56] ERROR nextflow.extension.OperatorImpl - @unknown

`java.lang.IllegalArgumentException: Argument of

file

function cannot be null`

Niklas Schandry

04/03/2025, 5:50 PM

Difficult to tell based on your description, my best guess is that you are missing an input or the samplesheet contains some mistake

Sadik

04/04/2025, 9:33 AM

Checked the samplesheet formated in csv as:

sample,ontreads,ref_fasta,ref_gff,short_F,short_R,paired

Niklas Schandry

04/04/2025, 9:34 AM

Copy code

sample,ontreads,hifireads,ref_fasta,ref_gff,shortread_F,shortread_R,paired
Sample1,sample1ont.fq.gz,sample1hifi.fq.gz,ref.fa,ref.gff,sample1_r1.fq.gz,sample1_r2.fq.gz,true

Niklas Schandry

04/04/2025, 9:34 AM

is the format that is required

Niklas Schandry

04/04/2025, 9:34 AM

so, try replacing

short_

with

shortread_

Sadik

04/04/2025, 9:57 AM

Thanks, got it working but caught by the following error

Sadik

04/04/2025, 9:58 AM

Copy code

Apr-04 10:50:49.757 [Actor Thread 29] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:POLISH:POLISH_MEDAKA:RUN_MEDAKA:MEDAKA (1)'

Caused by:
  Path value cannot be null

Niklas Schandry

04/04/2025, 10:01 AM

So, assembly worked but now medaka fails?

Sadik

04/04/2025, 10:01 AM

In job script I am skipping assembly and I think that might be the cause.

Niklas Schandry

04/04/2025, 10:01 AM

yeah that is the cause

Sadik

04/04/2025, 10:03 AM

Got it, thanks a lot. Is there an option to supply a custom assembled genome and do the QC, polishing and scaffolding ?

Niklas Schandry

04/04/2025, 10:04 AM

if you skip assembly (this was documented at some point), you have to change the samplesheet to inlcude a column

assembly

that contains your assembly

🙌 1

Sadik

04/04/2025, 10:05 AM

That' fab! Thanks a lot.

Niklas Schandry

04/04/2025, 10:05 AM

https://nf-co.re/genomeassembler/1.0.1/parameters/#skip_assembly

Niklas Schandry

04/04/2025, 10:06 AM

it shows up when you click on the help-text here...

Niklas Schandry

04/04/2025, 10:07 AM

I realize now that maybe

--skip_assembly

is used more often that I had anticipated

Sadik

04/04/2025, 10:09 AM

Sure, got it and I find also useful that a custom assembled genome can be assessed easily.

Niklas Schandry

04/04/2025, 10:10 AM

medaka

does not do any qc though, it does polishing with long-reads

👍 1

Sadik

04/04/2025, 10:12 AM

One more Q, sorry wanted to make sure I got it right. For ONT reads does it do hifiasm direct ont assembly from uncorrected reads ? (hifiasm --ont flag (v0.24.0-r70))

Sadik

04/04/2025, 10:13 AM

I see the option in the documentation but not sure whether it works that way.

Niklas Schandry

04/04/2025, 11:05 AM

Yes, if you use profile

ont_hifiasm

it will use

--ont

Niklas Schandry

04/04/2025, 11:08 AM

Or, generally if you use

ont

but not

hifi

and use

hifiasm

as the assembler

Sadik

04/11/2025, 2:20 PM

Running it for polishing with longreads (

--skip_assembly

) I got caught with

Cannot combine hifi and ont reads with flye

error.

Sadik

04/11/2025, 2:21 PM

Job was run as:

nextflow run nf-core/genomeassembler \

--input samplesheet.01.csv \

--outdir nf_gassembler \

-profile apptainer \

--skip_assembly TRUE \

--ont TRUE \

--hifi TRUE \

--short_reads TRUE \

--trim_short_reads FALSE \

--jellyfish FALSE \

--polish_pilon TRUE \

--polish_medaka TRUE \

--qc_reads FALSE \

--medaka_model r941_sup_plant_g610 \

--scaffold_longstitch TRUE \

--merqury TRUE \

--busco FALSE \

--busco_lineage embryophyta_odb10 \

--quast FALSE \

--lift_annotations FALSE

Sadik

04/11/2025, 2:21 PM

and .nextflow.log err

Sadik

04/11/2025, 2:22 PM

and .nextflow.log err:

Apr-11 14:45:51.622 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot combine hifi and ont reads with flye

Apr-11 14:45:51.642 [main] DEBUG nextflow.Session - The following nodes are still active:

[operator] splitCsv

[operator] map

[operator] map

Apr-11 14:45:51.649 [main] ERROR nextflow.cli.Launcher - @unknown

nextflow.exception.WorkflowScriptErrorException: Cannot combine hifi and ont reads with flye

at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)

at nextflow.Nextflow.error(Nextflow.groovy:226)

Sadik

04/11/2025, 2:25 PM

I am using pre-assembled genome to do the polishing with

--skip_assembly

option but it does look like it's trying to run the assembly process. I would appreciate any suggestion to sort this out.

Niklas Schandry

04/11/2025, 4:41 PM

You could try changing

--assembler

"hifiasm"

Niklas Schandry

04/11/2025, 4:42 PM

But this is a bug, I will try to fix it next week

Niklas Schandry

04/14/2025, 2:12 PM

This should be fixed in

dev

if you run with

-r dev

it should no longer give an error

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