run command again, but when I ran it again, the bug appeared

[wangguiqian]

Operating System

CentOS 7

Other Linux

CentOS 7

Workflow Version

v.23.10.1

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v1.3.0

CLI command run

Thank you for your help. I downloaded the 1.3.0 version of wf-pore-c according to your suggestion and ran it again, but I encountered an error at the beginning. The command I ran was as follows: nextflow run /Software/wf-pore-c-1.3.0/ --fastq ../raw_data/Pore-C_part1.fq.gz --ref ../Gh_genome.fa --cutter DpnII -c increase_memory.config --threads 30 --paired_end_minimum_distance 100 --paired_end_maximum_distance 200 --chunk_size 40000 --filter_pairs --paired_end --hi_c --out_dir PoreC_part1 -profile singularity -with-singularity '/Software/wf-pore-c-1.3.0/ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.sif' -with-trace -resume

And I used 30 cores to run this time, and my original fastq data was about 60G. Please look my data size: QQ_1729359835400

Below is the log file I ran. Please help me check it. Thank you. However, I read the log file later and it said that there was a problem with the fastcat command. It showed that the parameter setting of the fastcat command was wrong. I will share my log file with you. Please help me check it. Thank you. nextflow.log https://private-user-images.githubusercontent.com/48958211/378111108-106fb625-1c3b-45bf-979c-9e151b4980c0.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.F_LdoWJPOuarx-uIsFAdFvSK4enxk-w8eoEUH-YzN1o

Workflow Execution - CLI Execution Profile

None

What happened?

https://private-user-images.githubusercontent.com/48958211/378111108-106fb625-1c3b-45bf-979c-9e151b4980c0.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.F_LdoWJPOuarx-uIsFAdFvSK4enxk-w8eoEUH-YzN1o

Relevant log output

https://private-user-images.githubusercontent.com/48958211/378111108-106fb625-1c3b-45bf-979c-9e151b4980c0.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.F_LdoWJPOuarx-uIsFAdFvSK4enxk-w8eoEUH-YzN1o

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[wangguiqian]

When I get your suggest to run ,but I get fastcat commonand errors. Please look the Log file : [Uploading nextflow.log…]()

[sarahjeeeze]

Hi, thanks for using the workflow. The workflow requires multiple containers so defining it with -with-singularity ~/Software/wf-pore-c-1.3.0/ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.sif will not work. you will need to define each container in the config see how to do this - https://www.nextflow.io/docs/latest/container.html#singularity

[wangguiqian]

Hi, thanks for using the workflow. The workflow requires multiple containers so defining it with -with-singularity ~/Software/wf-pore-c-1.3.0/ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.sif will not work. you will need to define each container in the config see how to do this - https://www.nextflow.io/docs/latest/container.html#singularity

Please look my multiple containers seting on config-file .

The log file : wang.txt

[wangguiqian]

Hi, thanks for using the workflow. The workflow requires multiple containers so defining it with -with-singularity ~/Software/wf-pore-c-1.3.0/ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.sif will not work. you will need to define each container in the config see how to do this - https://www.nextflow.io/docs/latest/container.html#singularity

I had seting three containers to run .

[wangguiqian]

Hi, thanks for using the workflow. The workflow requires multiple containers so defining it with -with-singularity ~/Software/wf-pore-c-1.3.0/ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.sif will not work. you will need to define each container in the config see how to do this - https://www.nextflow.io/docs/latest/container.html#singularity

Please look the web :https://github.com/epi2me-labs/wf-pore-c/issues/72