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XiaoTaoWang / TADLib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
GNU General Public License v3.0
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error: "hitad: error: argument -d/--datasets: invalid datasets_convert value #20

Open Shaedeycool opened 2 years ago

Shaedeycool commented 2 years ago

I am new to HiTAD and HiC data. I am having trouble with the interpreting how the metadata text file should look. When I put the path to my mcool data generated from runHiC I get the error: "hitad: error: argument -d/--datasets: invalid datasets_convert value: 'coolers-hg38/rep2.mcool'". Some assistance would be greatly appreciated.

XiaoTaoWang commented 2 years ago

Can you show me the content of your metadata file?

Shaedeycool commented 2 years ago

res:int rep1:/lustre/magabothas/data/runHiC_workspace/22September2022/coolers-hg38/GM06990-HindIII-R1-filtered.mcool rep2:/lustre/magabothas/data/runHiC_workspace/22September2022/coolers-hg38/GM06990-HindIII-R2-filtered.mcool

XiaoTaoWang commented 2 years ago

Well, suppose you want to identify TADs at the 25kb resolution, then your metadata file should be::

res:25000
  rep1:/lustre/magabothas/data/runHiC_workspace/22September2022/coolers-hg38/GM06990-HindIII-R1-filtered.mcool::resolutions/25000
  rep2:/lustre/magabothas/data/runHiC_workspace/22September2022/coolers-hg38/GM06990-HindIII-R2-filtered.mcool::resolutions/25000
sfh1111 commented 5 months ago

Hi, I run into a similar issue.

I have change the metadata to:

res:25000 /home/labs/danielda/shdemf/m82_microC/merged.m82.200.mcool::resolutions/25000

Now I am getting the following error (in log file):

FileNotFoundError: [Errno 2] Unable to synchronously open file (unable to open file: name = '/home/labs/danielda/shdemf/m82_microC/:resolutions/25000', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)