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marbl / verkko

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how to specified the default partion, the canu could work with "gridOptions=" -q big"" , #219

Closed Jiangjiangzhang6 closed 6 months ago

Jiangjiangzhang6 commented 6 months ago

(verkko) [linfeifan@login2 05.hifi_ont]$ verkko --slurm -d /public/agis/yanjianbin_group/linfeifan/01.sanjianshan/01.assembly/05.hifi_ont/01.verrko/ --hifi $vcf --nano $ont --hic1 $hic1 --hic2 $hic2 --local-memory 2000 Launching bioconda verkko bioconda 1.4.1 Using snakemake 7.32.4. Using profile /public/home/linfeifan/miniconda3/envs/verkko/lib/verkko/profiles for setting default command line arguments. Building DAG of jobs... Using shell: /usr/bin/bash Provided cluster nodes: 1000 Job stats: job count

buildGraph 1 buildPackages 1 buildStore 1 combineConsensus 1 combineONT 1 combineOverlaps 1 combineOverlapsConfigure 1 combineTipsONT 1 configureFindErrors 1 configureOverlaps 1 copyFiles 1 correctHiFi 1 emptyfile 1 extractONT 1 fixErrors 1 generateLayoutContigsInputs 1 getCoverage 1 hicPhasing 1 indexBWA 1 layoutContigs 1 mergeBWA 1 prepCoverage 1 processGraph 1 processONT 1 runMashMap 1 runRukkiHIC 1 splitHIC 1 splitONT 1 splitTipsONT 1 transformBWA 1 untip 1 total 31

Select jobs to execute...

[Thu Dec 14 22:56:24 2023] localrule emptyfile: output: emptyfile jobid: 24 reason: Missing output files: emptyfile resources: mem_mb=1000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/tmp

[Thu Dec 14 22:56:24 2023] checkpoint splitHIC: input: /public/home/linfeifan/01.date/jjzhang/01.genome/01.raw_data/hic.all_R1.fastq.gz, /public/home/linfeifan/01.date/jjzhang/01.genome/01.raw_data/hic.all_R2.fastq.gz output: 8-hicPipeline/splitHIC.finished log: 8-hicPipeline/splitHIC.err jobid: 29 reason: Missing output files: 8-hicPipeline/splitHIC.finished threads: 8 resources: mem_mb=867008, mem_mib=826844, disk_mb=867008, disk_mib=826844, tmpdir=, job_id=1, n_cpus=8, mem_gb=16, time_h=24 DAG of jobs will be updated after completion.

sbatch: error: Batch job submission failed: No partition specified or system default partition

Jiangjiangzhang6 commented 6 months ago

hello, ask for your help, when i run the verkko with the data of hifi ,hic,and ont, but verkko show it didno't specified default partion, so how todo with it, i try the way as the canu ,but it's work, it would be happy for my to get your reply thank you

skoren commented 6 months ago

Slurm interactions in verkko is handled by snakemake. See #209 for a couple of options, you can edit the submit script in the installation so you don't have to always set a parameter on the system. You can also pass the extra options to slurm on the command line.

Jiangjiangzhang6 commented 6 months ago

Slurm interactions in verkko is handled by snakemake. See #209 for a couple of options, you can edit the submit script in the installation so you don't have to always set a parameter on the system. You can also pass the extra options to slurm on the command line.

thank you for your reply , I wild try it

skoren commented 6 months ago

Idle, I presume resolved as was in #209? Please re-open if you encounter other issues.