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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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error in running qcReport_make.Rmd #86

Open jielv opened 4 years ago

jielv commented 4 years ago

Hello,

I am testing hichipper on our server using the test data following the procedure described here: https://hichipper.readthedocs.io/en/latest/content/Usage.html

git clone https://github.com/aryeelab/hichipper.git cd hichipper/tests hichipper --out output1 yaml/one.yaml

It seems hichipper worked partially and here are the results I got:

_-rwxrwx--- 1 jlu Domain Users 0 Sep 8 19:30 d1.inter.loop_counts.bedpe -rwxrwx--- 1 jlu Domain Users 266506 Sep 8 19:30 d1.intra.loop_counts.bedpe -rwxrwx--- 1 jlu Domain Users 187439 Sep 8 19:30 d1.filt.intra.loopcounts.bedpe -rwxrwx--- 1 jlu Domain Users 22224 Sep 8 19:30 d1.anchors.bed -rwxrwx--- 1 jlu Domain Users 513 Sep 8 19:30 d1.stat -rwxrwx--- 1 jlu Domain Users 28203 Sep 8 19:31 d1-HiChIP.rds -rwxrwx--- 1 jlu Domain Users 247091 Sep 8 19:31 d1.interactions.all.mango -rwxrwx--- 1 jlu Domain Users 2238 Sep 8 19:31 output4.hichipper.log

Here is the error message I got:

_Taking input= as a system command ('zcat < resfrag/hg19_MboI_resfrag_chr22.bed.gz') and a variable has been used in the expression passed to input=. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Quitting from lines 167-190 (qcReport_make.Rmd) Error in { : task 1 failed - "Must subset rows with a valid subscript vector. x Subscript intra must be a simple vector, not a matrix." Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> %do% -> Execution halted Processing: d1 /hpcf/authorized_apps/rhel7apps/python/install/3.7.0/lib/python3.7/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)

It seems the pipeline failed at a later stage, when calling qcReport_make.Rmd. Currently, I have looked into all the required software listed here: https://hichipper.readthedocs.io/en/latest/content/Dependencies.html And found all of them have been installed on the server already.

Do you guys know what could be the potential problem? I appreciate any suggestions and comments.

Thanks, Jie

valderpan commented 2 years ago

Hi, I have encountered the same error reported, have you solved the problem? Thanks a lot.