Error executing process > 'pipeline:runPlannotate' Caused by: Missing output file(s) `*annotations.bed` expected by process `pipeline:runPlannotate`

[senidr]

Hi everytime i try to run this tool i keep getting the same error no matter what order of commands i use.

Would you please be able to help me see what is going wrong.

Thanks

[sarahjeeeze]

Hi, Thanks for pointing this out. The database we are using for the annotation is a little out of date. I am just working on a fix, will let you know when its ready.

[sarahjeeeze]

Hi, I think our most recent release v0.2.0 should have fixed this.

[zihengluo]

Hi, I downloaded the database from GitHub on 29th August 2022, but the same error still exists. I ran the pipeline on 31 plasmids and only one of them got this error .

[sarahjeeeze]

Hi, it looks like you are still using the old version. Try doing nextflow pull epi2me-labs/wf-clone-validation and running it again.

[zihengluo]

Thanks! The new version solved the error.

[Emmanuel1032967]

Hello. I am getting the same error. I have the latest version of the database. hecking fastq input. executor > local (457) executor > local (457) [3f/549b55] process > fastcat (90) [100%] 93 of 93 ✔ [31/41fc70] process > pipeline:checkIfEnoughReads (93) [100%] 93 of 93 ✔ [d2/f0d938] process > pipeline:assembleCore (53) [100%] 53 of 53 ✔ [19/4191da] process > pipeline:lookup_medaka_model (1) [100%] 1 of 1 ✔ [bd/c22ba7] process > pipeline:medakaPolishAssembly (53) [100%] 53 of 53 ✔ [71/119165] process > pipeline:downsampledStats (52) [100%] 53 of 53 ✔ [54/0aac62] process > pipeline:findPrimers (53) [100%] 53 of 53 ✔ [c6/b1874f] process > pipeline:medakaVersion [100%] 1 of 1 ✔ [b0/8b9840] process > pipeline:getVersions [100%] 1 of 1 ✔ [97/393825] process > pipeline:getParams [100%] 1 of 1 ✔ [c0/d78de9] process > pipeline:runPlannotate (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > pipeline:inserts - [- ] process > pipeline:report - [93/04e1fb] process > output (53) [100%] 53 of 53 ERROR ~ Error executing process > 'pipeline:runPlannotate (1)'

Caused by: Process pipeline:runPlannotate (1) terminated with an error exit status (141)

Command executed:

if [ -e "assemblies/OPTIONAL_FILE" ]; then assemblies="" else assemblies="--sequences assemblies/" fi workflow-glue run_plannotate $assemblies --database wf-clone-validation-db

Command exit status: 141

Command output: (empty)

Work dir: /home/grid/work/c0/d78de9af665fbc5cb7461322ca94de

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details

[sarahjeeeze]

Hi, did you run this cmd before the workflow?

wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-clone-validation/wf-clone-validation-db.tar.gz
tar -xzvf wf-clone-validation-db.tar.gz

[Emmanuel1032967]

Hello. I did

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From: Sarah Griffiths @.> Sent: Thursday, April 6, 2023 11:21:36 AM To: epi2me-labs/wf-clone-validation @.> Cc: Emmanuel Eziakor @.>; Comment @.> Subject: Re: [epi2me-labs/wf-clone-validation] Error executing process > 'pipeline:runPlannotate' Caused by: Missing output file(s) *annotations.bed expected by process pipeline:runPlannotate (Issue #5)

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Hi, did you run this cmd before the workflow?

wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-clone-validation/wf-clone-validation-db.tar.gz tar -xzvf wf-clone-validation-db.tar.gz

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[sarahjeeeze]

Hi, I need to investigate but have you tried running it without the db_directory parameter? The DB is now already included with the plannotate package, also are you running it with the standard profile docker? Just checking so I can try to recreate the error.

[sarahjeeeze]

Closing as no response but should also be fixed in the newer versions of the workflow as the db_directory input parameter no longer required.