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No qc reports #69
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Hi Eduardo,
I don’t think that there is an easy way to generate only these. It’s probably easiest to just rerun the tool with the software now installed.
… On May 17, 2019, at 3:49 PM, Eduardo R Martinez ***@***.***> wrote:
Hello,
I think hichipper worked partially as it generated the 4 of the 6 expected files mentioned in the outputs. In the output folder
ls -lrt
-rw-rw----+ 1 erafaelm feinbergLab 35054071 May 16 11:24 41.inter.loop_counts.bedpe
-rw-rw----+ 1 erafaelm feinbergLab 85338680 May 16 11:25 41.intra.loop_counts.bedpe
-rw-rw----+ 1 erafaelm feinbergLab 51004120 May 16 11:25 41.filt.intra.loop_counts.bedpe
-rw-rw----+ 1 erafaelm feinbergLab 3598647 May 16 11:25 41.anchors.bed
-rw-rw----+ 1 erafaelm feinbergLab 539 May 16 11:25 41.stat
-rw-rw----+ 1 erafaelm feinbergLab 5454 May 16 18:30 hichipper_output.hichipper.log
The hichipper.log has no errors:
less hichipper_output.hichipper.log
...
Thu May 16 18:30:15 EDT 2019: Creating QC report
Thu May 16 18:30:19 EDT 2019: Creating .rds and .mango files
Thu May 16 18:30:20 EDT 2019: Deleting temporary files
Thu May 16 18:30:22 EDT 2019: Done
However, while it ran the following was printed on the screen:
/users/erafaelm/venv/lib/python2.7/site-packages/hichipper/hichipperHelp.py:98: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load <https://msg.pyyaml.org/load> for full details.
m = yaml.load(f)
Quitting from lines 20-35 (qcReport_make.Rmd)
Error in library(networkD3) : there is no package called 'networkD3'
Calls: ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Execution halted
Error in library(diffloop) : there is no package called ‘diffloop’
Calls: suppressMessages -> withCallingHandlers
Execution halted
Consequently, I don't think the qc analysis ran. I've installed the libraries it requested. Do you know how I could generate the remaining files I should expect to be outputted by hichipper?
Thank you,
Eduardo
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Hello,
I think hichipper worked partially as it generated the 4 of the 6 expected files mentioned in the outputs. In the output folder
ls -lrt
-rw-rw----+ 1 erafaelm feinbergLab 35054071 May 16 11:24 41.inter.loop_counts.bedpe
-rw-rw----+ 1 erafaelm feinbergLab 85338680 May 16 11:25 41.intra.loop_counts.bedpe
-rw-rw----+ 1 erafaelm feinbergLab 51004120 May 16 11:25 41.filt.intra.loop_counts.bedpe
-rw-rw----+ 1 erafaelm feinbergLab 3598647 May 16 11:25 41.anchors.bed
-rw-rw----+ 1 erafaelm feinbergLab 539 May 16 11:25 41.stat
-rw-rw----+ 1 erafaelm feinbergLab 5454 May 16 18:30 hichipper_output.hichipper.log
The hichipper.log has no errors:
less hichipper_output.hichipper.log
...
Thu May 16 18:30:15 EDT 2019: Creating QC report
Thu May 16 18:30:19 EDT 2019: Creating .rds and .mango files
Thu May 16 18:30:20 EDT 2019: Deleting temporary files
Thu May 16 18:30:22 EDT 2019: Done
However, while it ran the following was printed on the screen:
/users/erafaelm/venv/lib/python2.7/site-packages/hichipper/hichipperHelp.py:98: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
m = yaml.load(f)
Quitting from lines 20-35 (qcReport_make.Rmd)
Error in library(networkD3) : there is no package called 'networkD3'
Calls: ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Execution halted
Error in library(diffloop) : there is no package called ‘diffloop’
Calls: suppressMessages -> withCallingHandlers
Execution halted
Consequently, I don't think the qc analysis ran. I've installed the libraries it requested. Do you know how I could generate the remaining files I should expect to be outputted by hichipper?
Thank you,
Eduardo
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