SamStudio8
commented
1 year ago Your error log contains the following message:
[2023-01-26 10:58:18.565] [error] CUDA device requested but no devices found.
This indicates Dorado cannot find a GPU which is required for basecalling. Does your computer have a GPU?
On Sat, 28 Jan 2023, 15:09 neurogenetics1, @.***> wrote:
What happened?
Hi,
I am getting an error when using a workflow EPI2ME in nextflow. I used the command as it is described on the GitHub page and –the help tutorial. It requires an input file and a model file. However, the dorado tool cannot find any of the available models, although I am using one of the suggested ones. There might be a configuration error. I have been trying to solve this problem for more than a week and have decided to get help. I will be grateful if you can solve this error. Operating System
ubuntu 20.04 Workflow Execution
Command line Workflow Execution - EPI2ME Labs Versions
nextflow/22.04.5 Workflow Execution - CLI Execution Profile
Singularity Workflow Version
wf-basecalling v0.2.0-g2d733e8 Relevant log output
Here is my command:
module load nextflow/22.04.5
module load singularity/3.10.5
cd AZ140021 export SINGULARITY_CACHEDIR=/data/nanopore/output
nextflow run -profile biowulf epi2me-labs/wf-basecalling --basecaller_cfg @.**@.)” --input /data/nanopore/AZ140021/20220307_1824_2D_PAI72310_c23d05c2/fast5_pass/ --ref /data/nanopore/ref/GRCh38_full_analysis_set_plus_decoy_hla.fa --dorado_ext fast5 --out_dir /data/nanopore/AZ140021/20220307_1824_2D_PAI72310_c23d05c2/output2023 --basecaller_basemod_threads 4
Output and error:
Core Nextflow options
revision : master
runName : voluminous_jones
containerEngine : singularity
launchDir : /vf/users/nanopore/AZ140021
workDir : /vf/users/nanopore/AZ140021/work
projectDir : /home/akcimenf2/.nextflow/22.04.5/assets/epi2me-labs/wf-basecalling
userName : akcimenf2
profile : biowulf
configFiles : /home/akcimenf2/.nextflow/22.04.5/assets/epi2me-labs/wf-basecalling/nextflow.config, /vf/users/nanopore/AZ140021/nextflow.config
Input Options
input : /data/nanopore/AZ140021/20220307_1824_2D_PAI72310_c23d05c2/fast5_pass/
ref : /data/nanopore/ref/GRCh38_full_analysis_set_plus_decoy_hla.fa
Output Options
out_dir : /data/nanopore/AZ140021/20220307_1824_2D_PAI72310_c23d05c2/output2023
Basecalling options
basecaller_cfg : @.**@.)
basecaller_basemod_threads: 4
Error executing process > 'wf_dorado:dorado (1)'
Caused by:
Process
wf_dorado:dorado (1)terminated with an error exit status (1)Command executed:
echo '***'
echo 'Available models:'
list-models | sed 's,^,- ,' | sed "s,${DRD_MODELS_PATH}/,,"
echo '***'
echo 'You selected:'
echo "Basecalling model: @.**@.)"
echo "Remora model : null"
echo '***'
echo 'A file open error below indicates that you have entered an unknown model name.'
echo 'It is possible the model you selected worked previously but has been updated to a new version.'
echo 'Resubmit this workflow with an appropriate model from the model list above.'
echo '***'
dorado basecaller @.**@.) . --device cuda:all | samtools view -b -o 0.ubam -
Command exit status:
1
Command output:
Available models:
@.**@.)
@.**@.)
@.**@.)
@.**@.)
@.**@*.**@*.**@.)
@.**@.)
@.**@*.**@*.**@.)
@.**@.)
@.**@*.**@*.**@.)
@.**@.)
@.**@.)
@.**@*.**@*.**@.)
@.**@.)
@.**@*.**@*.**@.)
@.**@.)
@.**@*.**@*.**@.)
@.***
You selected:
Basecalling model: @.**@.)
Remora model : null
A file open error below indicates that you have entered an unknown model name.
It is possible the model you selected worked previously but has been updated to a new version.
Resubmit this workflow with an appropriate model from the model list above.
Command error:
[2023-01-26 10:58:18.446] [info] > Creating basecall pipeline
[2023-01-26 10:58:18.565] [error] CUDA device requested but no devices found.
[main_samview] fail to read the header from "-".
Work dir:
/vf/users/nanopore/AZ140021/work/25/d1364160039a75f878052065d16636
Tip: when you have fixed the problem you can continue the execution adding the option
-resumeto the run command line— Reply to this email directly, view it on GitHub https://github.com/epi2me-labs/wf-basecalling/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIN6OWIM6EWFSAO25G6HV3WUUZA5ANCNFSM6AAAAAAUJWDKUU . You are receiving this because you are subscribed to this thread.Message ID: @.***>
neurogenetics1
What happened?
Hi,
I am getting an error when using a workflow EPI2ME in nextflow. I used the command as it is described on the GitHub page and –the help tutorial. It requires an input file and a model file. However, the dorado tool cannot find any of the available models, although I am using one of the suggested ones. There might be a configuration error. I have been trying to solve this problem for more than a week and have decided to get help. I will be grateful if you can solve this error.
Operating System
ubuntu 20.04
Workflow Execution
Command line
Workflow Execution - EPI2ME Labs Versions
nextflow/22.04.5
Workflow Execution - CLI Execution Profile
Singularity
Workflow Version
wf-basecalling v0.2.0-g2d733e8
Relevant log output