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I have run this pipeline with deduplicated bam as input and that worked. However, when I ran with fastq.gz as input, I encounter following error:
[2018-10-10 15:34:55,23] [info] Running with datab…
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The snakemake pipeline is for now only usable for PE sequencing, it would be good to have it to work for single end as well.
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A reminder for myself, the DAG output always has the same name. That's normally fine, but for ATAC-seq and ChIP-seq that'll end up in the DNA DAG getting overwritten. We should change the output names…
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OS or Platform: CentOS Linux release 7.4.1708
Cromwell/dxWDL version: cromwell-34.jar
Conda version: conda 4.3.30
I am trying to run the chip-seq pipeline on the test data (ENCSR936XTK) as per th…
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After the last community standup, there was an announcement about the phasing out of `project.json`.
Here are a few issues I see with that and would love some clarifications.
- [x] Most of the non-N…
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Hi there,
I attached the error printout of one sample run. Any one could help? Thanks a lot.
Huihui
Target exists: `/secondary/projects/shen/projects/2019_01_07_MSC_Lan/ATACseq/pepATAC/2_357…
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Hi, I am trying to run chipseq_pipeline using more than 2 replicates using the command as below. But it seems that the program can not take more than 2 replicates. I also attached part of the log fi…
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Hi ,
I used the command below to run the script in SCG cluster according the link you sent to me. It still tells me the bowtie index2 is missing. Could you have a look?
bds_scr atac.bds.BDS…
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Hello,
I'm trying to run workflow using the docker image, but I got the following error:
Unknown config attribute: wf_container.
Could you help me please?
## .nextflow.log
```
mai-16 15:25…
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Unsure why my task failed here. Any suggestion? There are 8 other runs like this too but here are the stdout and stderr files for the one that finished last.
Thank you very much for your help,
Aar…