# Why would native processes ( exec ) be resubmitted even though the hash inputs don't change?

**URL:** <https://community.seqera.io/t/why-would-native-processes-exec-be-resubmitted-even-though-the-hash-inputs-dont-change/2259>\
**Category:** Ask for help\
**Tags:** nextflow\
**Created:** [July 3, 2025, 12:12pm UTC](https://community.seqera.io/t/why-would-native-processes-exec-be-resubmitted-even-though-the-hash-inputs-dont-change/2259 "2025-07-03T12:12:55Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![mahesh.binzerpanchal](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mahesh.binzerpanchal/32/253_2.png) [@mahesh.binzerpanchal](https://community.seqera.io/u/mahesh.binzerpanchal)\
**Post date:** [July 3, 2025, 12:12pm UTC](https://community.seqera.io/t/why-would-native-processes-exec-be-resubmitted-even-though-the-hash-inputs-dont-change/2259/1 "2025-07-03T12:12:55Z")

</div>

I’m trying to figure out why a native process is occasionally resubmitting.

From one run the hashes are:

```auto
Jul-03 14:03:28.903 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [ASSEMBLY_REPORT:TOL_SEARCH (1)] cache hash: 96e3c94a530ae88fb7647046ec705b3e; mode: STANDARD; entries: 
  76ea2021cc55a873477f77be45e8a1fc [java.util.UUID] 8e358b4c-7f8d-4421-8742-0a77a3f8c4d6 
  bdf226854332f21139e1ddac952e22ba [java.lang.String] ASSEMBLY_REPORT:TOL_SEARCH 
  f13fc1b539c963cfd9f7a5eda57f24b3 [java.lang.String] def args = task.ext.args ?: ''
    def response = new URL("https://id.tol.sanger.ac.uk/api/v2/species?taxonomyId=$taxid").text
    def lazy_json = new groovy.json.JsonSlurper().parseText(response)
    json = [
        tol_id: lazy_json.species[0]['tolIds'][0]?.tolId?: "No ToL ID",
        species: lazy_json.species[0]['scientificName'],
        class: lazy_json.species[0]['taxaClass'],
        order: lazy_json.species[0]['order'],
    ]
 
  16cb95a8f5388c13899a651695911162 [java.lang.String] taxid 
  dec56b9915c1138e7cd4677f712b5833 [java.lang.Integer] 7227 
  4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ 
  16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true 
  eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] 

Jul-03 14:03:28.922 [Task submitter] INFO nextflow.Session - [c1/d3eb41] Submitted process > ASSEMBLY_REPORT:TOL_SEARCH (Taxid: 7227)

```

and from the following run:

```auto
Jul-03 14:04:33.476 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [ASSEMBLY_REPORT:TOL_SEARCH (1)] cache hash: 96e3c94a530ae88fb7647046ec705b3e; mode: STANDARD; entries: 
  76ea2021cc55a873477f77be45e8a1fc [java.util.UUID] 8e358b4c-7f8d-4421-8742-0a77a3f8c4d6 
  bdf226854332f21139e1ddac952e22ba [java.lang.String] ASSEMBLY_REPORT:TOL_SEARCH 
  f13fc1b539c963cfd9f7a5eda57f24b3 [java.lang.String] def args = task.ext.args ?: ''
    def response = new URL("https://id.tol.sanger.ac.uk/api/v2/species?taxonomyId=$taxid").text
    def lazy_json = new groovy.json.JsonSlurper().parseText(response)
    json = [
        tol_id: lazy_json.species[0]['tolIds'][0]?.tolId?: "No ToL ID",
        species: lazy_json.species[0]['scientificName'],
        class: lazy_json.species[0]['taxaClass'],
        order: lazy_json.species[0]['order'],
    ]
 
  16cb95a8f5388c13899a651695911162 [java.lang.String] taxid 
  dec56b9915c1138e7cd4677f712b5833 [java.lang.Integer] 7227 
  4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ 
  16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true 
  eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] 

Jul-03 14:04:33.497 [Task submitter] INFO nextflow.Session - [c1/d3eb41] Submitted process > ASSEMBLY_REPORT:TOL_SEARCH (Taxid: 7227)

```

I should say before I resume the next run I do

```auto
nextflow clean -f -before $( nextflow log -q | tail -n 1)

```

and then the native process is resubmitted. If I don’t do this, it’ll take the cached result from an earlier run.

---

<div class="post-metadata">

**Author:** ![mahesh.binzerpanchal](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mahesh.binzerpanchal/32/253_2.png) [@mahesh.binzerpanchal](https://community.seqera.io/u/mahesh.binzerpanchal)\
**Post date:** [July 4, 2025, 12:48pm UTC](https://community.seqera.io/t/why-would-native-processes-exec-be-resubmitted-even-though-the-hash-inputs-dont-change/2259/2 "2025-07-04T12:48:56Z")

</div>

It seems this might be an issue with `nextflow clean`

> <https://github.com/nextflow-io/nextflow/issues/6246>
>
> \## Bug report 
> 
> I have a native process that resubmits itself on \`-resume\` even …though the inputs don't change, but only if I've cleaned previous executions.
> 
> \### Expected behavior and actual behavior
> 
> I expect the process to be cached. Nextflow only uses a cached version if I don't clean previous runs. 
> 
> \### Steps to reproduce the problem
> 
> https://github.com/NBISweden/Earth-Biogenome-Project-pilot
> 
> \`\`\`
> nextflow run main.nf -profile docker,test -resume
> nextflow clean -f -before $( nextflow log -q | tail -n 1 ) && find work/ -type d -empty -delete
> nextflow run main.nf -profile docker,test -resume
> \`\`\`
> 
> If I don't clean, then the process uses a cached hit.
> 
> \### Program output 
> 
> I posted the question in the community forum initially:
> https://community.seqera.io/t/why-would-native-processes-exec-be-resubmitted-even-though-the-hash-inputs-dont-change/2259
> 
> hashes from run1
> \`\`\`
> Jul-03 14:03:28.903 \[Actor Thread 5\] INFO nextflow.processor.TaskProcessor - \[ASSEMBLY\_REPORT:TOL\_SEARCH (1)\] cache hash: 96e3c94a530ae88fb7647046ec705b3e; mode: STANDARD; entries: 
> 76ea2021cc55a873477f77be45e8a1fc \[java.util.UUID\] 8e358b4c-7f8d-4421-8742-0a77a3f8c4d6 
> bdf226854332f21139e1ddac952e22ba \[java.lang.String\] ASSEMBLY\_REPORT:TOL\_SEARCH 
> f13fc1b539c963cfd9f7a5eda57f24b3 \[java.lang.String\] def args = task.ext.args ?: ''
> def response = new URL("https://id.tol.sanger.ac.uk/api/v2/species?taxonomyId=$taxid").text
> def lazy\_json = new groovy.json.JsonSlurper().parseText(response)
> json = \[
> tol\_id: lazy\_json.species\[0\]\['tolIds'\]\[0\]?.tolId?: "No ToL ID",
> species: lazy\_json.species\[0\]\['scientificName'\],
> class: lazy\_json.species\[0\]\['taxaClass'\],
> order: lazy\_json.species\[0\]\['order'\],
> \]
>  
> 16cb95a8f5388c13899a651695911162 \[java.lang.String\] taxid 
> dec56b9915c1138e7cd4677f712b5833 \[java.lang.Integer\] 7227 
> 4f9d4b0d22865056c37fb6d9c2a04a67 \[java.lang.String\] $ 
> 16fe7483905cce7a85670e43e4678877 \[java.lang.Boolean\] true 
> eab359affdb9334848cc02803d7db724 \[java.util.HashMap$EntrySet\] \[task.ext.args=null\] 
> 
> Jul-03 14:03:28.922 \[Task submitter\] INFO nextflow.Session - \[c1/d3eb41\] Submitted process \> ASSEMBLY\_REPORT:TOL\_SEARCH (Taxid: 7227)
> \`\`\`
> and hashes from run2
> \`\`\`
> Jul-03 14:04:33.476 \[Actor Thread 2\] INFO nextflow.processor.TaskProcessor - \[ASSEMBLY\_REPORT:TOL\_SEARCH (1)\] cache hash: 96e3c94a530ae88fb7647046ec705b3e; mode: STANDARD; entries: 
> 76ea2021cc55a873477f77be45e8a1fc \[java.util.UUID\] 8e358b4c-7f8d-4421-8742-0a77a3f8c4d6 
> bdf226854332f21139e1ddac952e22ba \[java.lang.String\] ASSEMBLY\_REPORT:TOL\_SEARCH 
> f13fc1b539c963cfd9f7a5eda57f24b3 \[java.lang.String\] def args = task.ext.args ?: ''
> def response = new URL("https://id.tol.sanger.ac.uk/api/v2/species?taxonomyId=$taxid").text
> def lazy\_json = new groovy.json.JsonSlurper().parseText(response)
> json = \[
> tol\_id: lazy\_json.species\[0\]\['tolIds'\]\[0\]?.tolId?: "No ToL ID",
> species: lazy\_json.species\[0\]\['scientificName'\],
> class: lazy\_json.species\[0\]\['taxaClass'\],
> order: lazy\_json.species\[0\]\['order'\],
> \]
>  
> 16cb95a8f5388c13899a651695911162 \[java.lang.String\] taxid 
> dec56b9915c1138e7cd4677f712b5833 \[java.lang.Integer\] 7227 
> 4f9d4b0d22865056c37fb6d9c2a04a67 \[java.lang.String\] $ 
> 16fe7483905cce7a85670e43e4678877 \[java.lang.Boolean\] true 
> eab359affdb9334848cc02803d7db724 \[java.util.HashMap$EntrySet\] \[task.ext.args=null\] 
> 
> Jul-03 14:04:33.497 \[Task submitter\] INFO nextflow.Session - \[c1/d3eb41\] Submitted process \> ASSEMBLY\_REPORT:TOL\_SEARCH (Taxid: 7227)
> \`\`\`
> 
> \### Environment 
> 
> \* Nextflow version: 25.04.4
> \* Java version: \[?\]
> \* Operating system: \[macOS, Linux, etc\]
> \* Bash version: (use the command \`$SHELL --version\`)
> 
> \### Additional context
> 
> (Add any other context about the problem here)

---

<div class="post-metadata">

**Author:** ![mahesh.binzerpanchal](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mahesh.binzerpanchal/32/253_2.png) [@mahesh.binzerpanchal](https://community.seqera.io/u/mahesh.binzerpanchal)\
**Post date:** [July 11, 2025, 12:49pm UTC](https://community.seqera.io/t/why-would-native-processes-exec-be-resubmitted-even-though-the-hash-inputs-dont-change/2259/3 "2025-07-11T12:49:35Z")

</div>

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.