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Error GCP/S tutorial #25

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amnahsiddiqa opened this issue Jan 7, 2024 · 0 comments
Open

Error GCP/S tutorial #25

amnahsiddiqa opened this issue Jan 7, 2024 · 0 comments

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@amnahsiddiqa
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I have been trying to follow GCP/S tutorial to use this proof of concept pipeline https://cloud.google.com/batch/docs/nextflow#command-line using gcb profile. My GCP credentials looks like working fine. But I am getting the error as follows. I would appreciate any help here.

amnah_cchmc@cloudshell:~/rnaseq-nf (pmod-410207)$ ../nextflow run nextflow-io/rnaseq-nf -profile gcb 

Output error:

N E X T F L O W  ~  version 23.04.1
Launching `https://github.com/nextflow-io/rnaseq-nf` [stoic_kare] DSL2 - revision: 8253a586cc [master]
Jan 07, 2024 9:45:35 PM com.google.auth.oauth2.DefaultCredentialsProvider warnAboutProblematicCredentials
WARNING: Your application has authenticated using end user credentials from Google Cloud SDK. We recommend that most server applications use service accounts instead. If your application continues to use end user credentials from Cloud SDK, you might receive a "quota exceeded" or "API not enabled" error. For more information about service accounts, see https://cloud.google.com/docs/authentication/.
 R N A S E Q - N F   P I P E L I N E
 ===================================
 transcriptome: gs://rnaseq-nf/data/ggal/transcript.fa
 reads        : gs://rnaseq-nf/data/ggal/gut_{1,2}.fq
 outdir       : results
 
Uploading local `bin` scripts folder to gs://gcpbucket_toy/testres/tmp/9a/b274c07f0819f8241f8408664ff288/bin
executor >  google-batch (2)
[ba/0829c0] process > RNASEQ:INDEX (transcript)     [100%] 1 of 1 ✔
[a6/bad50e] process > RNASEQ:FASTQC (FASTQC on gut) [  0%] 0 of 1
[-        ] process > RNASEQ:QUANT                  -
[-        ] process > MULTIQC                       -
ERROR ~ Error executing process > 'RNASEQ:QUANT (1)'

Caused by:
  Oops.. something went wrong while creating task 'RNASEQ:QUANT' unique id -- Offending keys: [
 - type=java.util.UUID value=12d80190-0c61-4bc8-a7d3-3e24a9340bfd, 
 - type=java.lang.String value=RNASEQ:QUANT, 
 - type=java.lang.String value="""
    salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
    """
executor >  google-batch (2)
[ba/0829c0] process > RNASEQ:INDEX (transcript)     [100%] 1 of 1 ✔
[-        ] process > RNASEQ:FASTQC (FASTQC on gut) [  0%] 0 of -1 ✔
[-        ] process > RNASEQ:QUANT                  -[-        ] process > MULTIQC                       -
ERROR ~ Error executing process > 'RNASEQ:QUANT (1)'

Caused by:
  Oops.. something went wrong while creating task 'RNASEQ:QUANT' unique id -- Offending keys: [ - type=java.util.UUID value=12d80190-0c61-4bc8-a7d3-3e24a9340bfd, 
 - type=java.lang.String value=RNASEQ:QUANT, 
 - type=java.lang.String value="""
    salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
    """
, 
 - type=java.lang.String value=quay.io/nextflow/rnaseq-nf:v1.2.1, 
 - type=java.lang.String value=index, 
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/testres/ba/0829c0f5dfe57924224b6e20581701/index, storePath:/testres/ba/0829c0f5dfe57924224b6e20581701/index, stageName:index)],  - type=java.lang.String value=pair_id, 
 - type=java.lang.String value=gut, 
 - type=java.lang.String value=reads, 
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/data/ggal/gut_1.fq, storePath:/data/ggal/gut_1.fq, stageName:gut_1.fq), FileHolder(sourceObj:/data/ggal/gut_2.fq, storePath:/data/ggal/gut_2.fq, stageName:gut_2.fq)], 
 - type=java.lang.String value=$, 
 - type=java.lang.Boolean value=true, 
 - type=java.util.HashMap$EntrySet value=[task.cpus=null]]


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

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