Cannot get property 'fasta' on null object

[Thomieh73]

Hi, I am trying out the MAG pipeline on a small set of samples, just to check if I can get it to work with my data. I get an error before the pipeline starts and I wonder if that has to do with my input or not.

This is my command:

nextflow run nf-core/mag -r 3.0.2 -profile apptainer \
	-c saga_mag.config -work-dir $USERWORK/nf_mag -resume \
	--input samplesheet_small.csv \
	--outdir /cluster/projects/nn10070k/projects/phagedrive/pd_data_control/results/20240726_MAG_results \
	--reads_minlength 50 \
	--host_genome ../../viral_mask_results/masked_host_db/combined_hosts_phix.fna.gz \
	--bbnorm FALSE \
	--kraken2_db /cluster/projects/nn10070k/databases/kraken2_pluspfp_05.06.2024 \
	--cat_db_generate \
	--save_cat_db \
	--run_virus_identification

and I get this error from nextflow after it has pulled the pipeline:

Nextflow 24.04.3 is available - Please consider updating your version to it
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/mag` [mad_mestorf] DSL2 - revision: bb74c4695d [3.0.2]
ERROR ~ Cannot get property 'fasta' on null object

 -- Check script '/cluster/home/thhaverk/.nextflow/assets/nf-core/mag/./workflows/mag.nf' at line: 87 or see '.nextflow.log' file for more details

in the .nextflow.log I find this:

Jul-26 14:50:44.572 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot get property 'fasta' on null object
Jul-26 14:50:44.594 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.NullPointerException: Cannot get property 'fasta' on null object
        at org.codehaus.groovy.runtime.NullObject.getProperty(NullObject.java:60)
        at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:190)
        at org.codehaus.groovy.runtime.callsite.NullCallSite.getProperty(NullCallSite.java:46)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGetProperty(AbstractCallSite.java:329)
        at Script_a511e04e7e5ccdee.runScript(Script_a511e04e7e5ccdee:87)
        at nextflow.script.BaseScript.run0(BaseScript.groovy:144)
        at nextflow.script.BaseScript.run(BaseScript.groovy:192)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:222)
        at nextflow.script.IncludeDef.memoizedMethodPriv$loadModule0PathMapSession(IncludeDef.groovy:151)
        at nextflow.script.IncludeDef.access$0(IncludeDef.groovy)
        at nextflow.script.IncludeDef$__clinit__closure2.doCall(IncludeDef.groovy)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at groovy.lang.Closure.call(Closure.java:427)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.lambda$call$0(Memoize.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:113)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.call(Memoize.java:136)
        at nextflow.script.IncludeDef.loadModule0(IncludeDef.groovy)
        at nextflow.script.IncludeDef.load0(IncludeDef.groovy:123)
        at nextflow.script.IncludeDef$load0$1.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at Script_976cceeb3c81f6ed.runScript(Script_976cceeb3c81f6ed:20)
        at nextflow.script.BaseScript.run0(BaseScript.groovy:144)
        at nextflow.script.BaseScript.run(BaseScript.groovy:192)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236)
        at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:242)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:137)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
        at nextflow.cli.Launcher.run(Launcher.groovy:500)
        at nextflow.cli.Launcher.main(Launcher.groovy:672)

[jfy133]

Hi @Thomieh73 could you try either wrapping your --host_genome in quotes, or giving it a full path?

[Thomieh73]

I think I solved this by using the launch button on the nf-core page. That created a params.json file that I could use.

I did however, try to run Mag with the test profile, to see if I could get that to work on our HPC cluster with slurm. That fails. It is a bit similar to the problems described here in issue #554.

[jfy133]

I think I solved this by using the launch button on the nf-core page. That created a params.json file that I could use.

Ok interesting. I'm guessing it was due to the paths as I think launch tries to resolve the whole thing(?) or at least quotes itm

I did however, try to run Mag with the test profile, to see if I could get that to work on our HPC cluster with slurm. That fails. It is a bit similar to the problems described here in issue #554.

Feel free to make another issue, the problems on that issue were never entirely clear