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c-guzman / cipher-workflow-platform

A data processing platform for ChIP-seq, RNA-seq, MNase-seq, DNase-seq, ATAC-seq and GRO-seq datasets. Please ignore information on cipher.readthedocs.io, it is currently out of date. Follow information in README.
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Atac-Seq #11

Open jsalignon opened 6 years ago

jsalignon commented 6 years ago

Hi,

Thanks for this pipeline.

I was trying to use it on atac-seq data. I got the following error message: Caused by: Process bamCoverage (1) terminated with an error exit status (127) Command executed: null Checking at the code I found that there is no options for atac seq in this process. I added it line 1016 this way: if (params.mode == "chip" || params.mode == "dnase" || params.mode == "atac") However I am not sure this is correct.

By the way I think the provided example (H3K4me3.500k) lacks instruction: what command to launch? I guess it is chip seq but in which organism? Including the corresponding gtf and fasta file could be nice.

Thanks, Jerome

c-guzman commented 6 years ago

Silly mistake, great catch! Will update this today, and you're completely right. The genome for those datasets are human. Will update that information.

On Jan 20, 2018 5:15 AM, "Bioninbo" notifications@github.com wrote:

Hi,

Thanks for this pipeline.

I was trying to use it on atac-seq data. I got the following error message: Caused by: Process bamCoverage (1) terminated with an error exit status (127) Command executed: null Checking at the code I find that there is no options for atac seq in this process. I added it line 1016 this way: if (params.mode == "chip" || params.mode == "dnase" || params.mode == "atac") However I am not sure this is correct.

By the way I think the provided example (H3K4me3.500k) lacks instruction: what command to launch? I guess it is chip seq but in which organism? Including the corresponding gtf and fasta file could be nice.

Thanks, Jerome

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rdbcasillas commented 6 years ago

Has this error been fixed? I get the exact same error while performing ATAC seq analysis. 

May-13 15:23:56.444 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .c
ommand.run
May-13 15:23:56.446 [Task submitter] INFO  nextflow.Session - [1a/b663ef] Submitted process > estimate_fragment_s
ize (2)
May-13 15:23:56.743 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'bamCoverag
e (1)'

Caused by:
  Process `bamCoverage (1)` terminated with an error exit status (127)

Command executed:

  null

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: null: command not found

Let me know if more information is required to understand the source of this error. This information is from .nextflow.log file.