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## **Describe the bug**
I tried to run this pipeline multiple times, and it kept getting stalled at task=atac.read_genome_tsv:-1. But there's no error message. It only stopped when timeout.
f1ce-4…
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## **Describe the bug**
I have followed the instructions for installation of the pipeline using conda, the installation was successfully completed but when I run it I get the following error:
Sta…
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I am running pipeline version: v1.9.2. My pipeline runs till atac.macs2_signal_track, then the next atac.qc_report is not triggered. I have following questions about the pipeline:
> 1. Is there …
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Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure wa…
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I installed the latest version of caper and the ATAC-seq pipeline, and the pipeline is stalled at the read_genome step. It has been running for multiple days without progress. I have been running it o…
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Hi,
first of all, thank you for providing a wonderful tool. I ran the ATAC-seq analysis using the pipeline on data as shown below
1. control -> no replicate
2. sample -> 2 biological replicate.
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# 1. 可能是 ATAC-seq 方法的原始文献 (nature methods, 2023)
https://www.nature.com/articles/nmeth.2688
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-bi…
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Hi there,
I have a problem running the pipeline which I have set up on a SLURM HPC. It had worked previously and I used it regularly for the best part of a year. However it stopped working after a …
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## **Describe the bug**
caper.cromwell.WomtoolValidationFailed: RC=1
## **OS/Platform**
- OS/Platform: [e.g. Ubuntu 18.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
- Conda version: 4.13…
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This error occurs while using the atac-seq-pipeline but I do not believe this is specific to that. When using Singularity, relative paths to local input files do not get included in the Singularity bi…