Error fromIndex = -1

[aubinthomas]

Description of the bug

Hello,

I just ran one of my test samples that works on v1.2.2, but not on v2 of the pipeline.

The pipeline works perfectly but after MACS step it throws an error :

fromIndex = -1

 -- Check script 'workflow/./workflows/chipseq.nf' at line: 555 or see '.nextflow.log' file for more details

the .nextflow.log contains this error:

Oct-05 17:11:29.570 [Actor Thread 5] ERROR nextflow.extension.OperatorEx - @unknown
java.lang.RuntimeException: java.nio.channels.ClosedByInterruptException
        at nextflow.sort.BigSort.sort(BigSort.java:255)
        at nextflow.file.SortFileCollector.makeHash(SortFileCollector.groovy:248)
        at nextflow.file.FileCollector.saveTo(FileCollector.groovy:239)
        at nextflow.file.FileCollector$saveTo.call(Unknown Source)
        at nextflow.extension.CollectFileOp.emitItems(CollectFileOp.groovy:191)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1268)
        at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1048)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1142)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:428)
        at groovy.lang.Closure$call.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at nextflow.extension.DataflowHelper$3.afterStop(DataflowHelper.groovy:255)
        at groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324)
        at groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59)
        at sun.reflect.GeneratedMethodAccessor195.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)

Thanks

Command used and terminal output

$ ./nextflow-21.10.4-all run workflow/main.nf --input design.csv --genome GRCh38 -profile singularity,mesolr --single_end --outdir 'result' --read_length 75

Relevant files

design.csv
nextflow.log

System information

nextflow-21.10.4-all
HPC
slurm
Singularity
nf-core/chipseq-2.0.0
java version "1.8.0_112", Java(TM) SE Runtime Environment (build 1.8.0_112-b15), Java HotSpot(TM) 64-Bit Server VM (build 25.112-b15, mixed mode)

[dshinzie]

This thread looks like it discusses the issue: https://nfcore.slack.com/archives/CFP55NZ5G/p1669741955467179?thread_ts=1669721950.821779&cid=CFP55NZ5G

[aubinthomas]

Thanks, that 's it!

[aydemiro]

Edit: It looks like sample names must include replicate numbers even if there are no replicates and they must follow a specific format: an underscore followed by at least a number or a letter and number. For example, sample1_1 or sample1_R1 or sample1_REP1 but not sample1.

Original question: I am having a similar error but I cannot access the referenced slack thread. Can you share what the issue and solution are here if possible?

Thanks in advance

[JoseEspinosa]

Essentially, you will need to rename your samples to add the replicate using a _ followed by a number _1 or _REP1 or _R1 e.g.:

sample,fastq_1,fastq_2,antibody,control
sample_1_R1,file1,file2,H3K27ac,input-15min-12Aug_1
sample_2_R1,file1,file2,H3K27ac,input-1h-12Aug_1
sample_3_R1,file1,file2,,

I will open an issue since this is probably not the clearest way of doing it for improving this in the next iteration of the pipeline