Hi all,
I have been running the nf-core/rnaseq pipeline over the past months without issues. Now, I get this error message when attempting to run the same workflow that succeeded two weeks ago:
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (8)'
Caused by:
Wave invalid response: POST https://wave.seqera.io/v1alpha2/container [400] {"message":"Container image 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0' does not exist or access is not authorized"}
I have checked, and the container image exists, so I assume that it is an authorisation issue of my access.
This is how I call the run, and the stdout messages:
$ nextflow -c "FILE_PATH_TO/custom_nextflow.config" run nf-core/rnaseq -r 3.14.0 '--input=FILE_PATH_TO/samplesheet.csv' '--outdir=FILE_PATH_TO/results' '--fasta=FILE_PATH_TO/GENOME_FILE.dna.fa' '--gtf=FILE_PATH_TO/GENOME_FILE.gtf'
N E X T F L O W ~ version 24.10.0
Launching `https://github.com/nf-core/rnaseq` [chaotic_majorana] DSL2 - revision: b89fac3265 [3.14.0]
WARN: The following invalid input values have been detected:
* --awsqueue: ec2-rnaseq
* --awsregion: MY_REGION
* --awscli: /usr/local/bin/aws
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Multiple config files detected!
Please provide pipeline parameters via the CLI or Nextflow '-params-file' option.
Custom config files including those provided by the '-c' Nextflow option can be
used to provide any configuration except for parameters.
Docs: https://nf-co.re/usage/configuration#custom-configuration-files
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/rnaseq v3.14.0-gb89fac3
------------------------------------------------------
Core Nextflow options
revision : 3.14.0
runName : chaotic_majorana
containerEngine : docker
launchDir : /data/rnaseq/wave_access/prev_runs
workDir : FILE_PATH/wdir
projectDir : /home/ubuntu/.nextflow/assets/nf-core/rnaseq
userName : ubuntu
profile : standard
configFiles :
Input/output options
input : FILE_PATH_TO/samplesheet.csv
outdir : FILE_PATH_TO/results
Reference genome options
fasta : FILE_PATH_TO/GENOME_FILE.dna.fa
gtf : FILE_PATH_TO/GENOME_FILE.gtf
Alignment options
min_mapped_reads : 5
Institutional config options
config_profile_description: AWSBATCH Cloud Profile
config_profile_contact : My Name
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/rnaseq for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.1400710
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/rnaseq/blob/00f924cf92a986a842bb352b3c4ae379c773c989/CITATIONS.md
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER -
... -
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (8)'
Caused by:
Wave invalid response: POST https://wave.seqera.io/v1alpha2/container [400] {"message":"Container image 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0' does not exist or access is not authorized"}
-- Check '.nextflow.log' file for details
-[nf-core/rnaseq] Pipeline completed with errors
And here is my costom config nextflow file:
params {
config_profile_description = 'AWSBATCH Cloud Profile'
config_profile_contact = 'My_Name'
awsqueue = 'aQueueThatWorkedPreviously'
awsregion = 'aRegionThatWorkedPreviously'
awscli = 'PathToClient'
}
timeline {
overwrite = true
}
report {
overwrite = true
}
trace {
overwrite = true
}
dag {
overwrite = true
}
docker {
enabled = true
}
fusion {
enabled = true
exportStorageCredentials = true
}
wave {
enabled = true
}
workDir = 'path_to/wdir'
process.executor = 'awsbatch'
process.queue = params.awsqueue
aws.region = params.awsregion
aws.batch.cliPath = params.awscli
The issue is reproducible on different AWS VMs and the container image can be dowloaded by running docker pull quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0, so I think that it might be an issue with permissions. It is odd, because exactly the same workflow worked two weeks ago.
Has anyone come across this issue before? I would greatly appreciate any input!
edit: I have tried the newest version of the nf-core/rnaseq workflow (3.17.0), but get the same error. I also checked other nf-core workflows which previously succeeded and now raise the same error