`nextflow clean` throws `Unexpected error [EOFException]` when attempting to clean previous runs

[MatteoSchiavinato]

Bug report

After a successful run of my pipeline, I am trying to clean the workspace from previous runs. I'm doing so using nextflow clean -f -before nauseous_cajal, which is the mnemonic of the latest run.

Expected behavior and actual behavior

I would expect this to work seamlessly by removing the previous runs and leaving only "nauseous_cajal" in the nextflow log. However, when running the command (regardless of -f or -n) it throws out this error:

Unexpected error [EOFException]

Steps to reproduce the problem

I am simply trying to clean up previous runs, something I did with this workflow for the past months every now and then, and in general has never thrown out errors before in the system I use.

I have run nextflow -log log clean -f -before nauseous_cajal as suggested in the nextflow gitter chat to another user some time ago, and this is the produced log:

ene-28 13:47:54.839 [main] DEBUG nextflow.cli.Launcher - $> nextflow -log log clean -f -before nauseous_cajal
ene-28 13:47:55.176 [main] ERROR nextflow.cli.Launcher - null
java.io.EOFException: null
        at java.io.RandomAccessFile.readBoolean(RandomAccessFile.java:644)
        at nextflow.CacheDB.eachRecord(CacheDB.groovy:272)
        at nextflow.cli.CmdClean.cleanup(CmdClean.groovy:116)
        at nextflow.cli.CmdClean.access$0(CmdClean.groovy)
        at nextflow.cli.CmdClean$_run_closure1.doCall(CmdClean.groovy:93)
        at nextflow.cli.CmdClean$_run_closure1.call(CmdClean.groovy)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2318)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2303)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2344)
        at nextflow.cli.CmdClean.run(CmdClean.groovy:93)
        at nextflow.cli.Launcher.run(Launcher.groovy:475)
        at nextflow.cli.Launcher.main(Launcher.groovy:657)

nextflow.log

Environment

• Nextflow version: 21.04.3 build 5560
• Java version: openjdk version "1.8.0_161"
• Operating system: SUSE Linux Enterprise Server 12 SP2
• Bash version: 4.3.42(1)-release (x86_64-suse-linux-gnu)

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[pditommaso]

we have to look into this

[mribeirodantas]

I tried and couldn't reproduce it.

➜  ~ NXF_VER=21.04.3 nextflow clean -f -before pedantic_heisenberg
CAPSULE: Downloading dependency org.slf4j:log4j-over-slf4j:jar:1.7.25
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:3.0.7
CAPSULE: Downloading dependency io.nextflow:nextflow:jar:21.04.3
CAPSULE: Downloading dependency org.slf4j:slf4j-api:jar:1.7.25
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:21.04.3
CAPSULE: Downloading dependency org.jsoup:jsoup:jar:1.11.2
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:3.0.7
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:3.0.7
CAPSULE: Downloading dependency ch.qos.logback:logback-core:jar:1.1.11
CAPSULE: Downloading dependency org.slf4j:jul-to-slf4j:jar:1.7.25
CAPSULE: Downloading dependency ch.qos.logback:logback-classic:jar:1.1.11
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:21.04.3
CAPSULE: Downloading dependency org.yaml:snakeyaml:jar:1.18
CAPSULE: Downloading dependency org.slf4j:jcl-over-slf4j:jar:1.7.25
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:3.0.7
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:3.0.7
Removed /Users/mribeirodantas/work/b8/7c6c916a3e9701d22ddab4b30b8c03
Removed /Users/mribeirodantas/work/c8/185ae5b1426b02ef3ec44adfa818f4
Removed /Users/mribeirodantas/work/10/056cfb18a02b60dacf7b6a395d4598
Removed /Users/mribeirodantas/work/c8/d40ca0feed3aff003291255bc4974e

[pditommaso]

It can be closed then