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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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Error in hichipper Rscript qc Report #58

Open boconnell89 opened 6 years ago

boconnell89 commented 6 years ago

hichipper consistently crashes at the qcReport step (even with individual libraries). I've pasted the error code below:

Thu Nov 8 17:29:19 PST 2018: Total number of reads in anchors: 2544455 Thu Nov 8 17:29:21 PST 2018: Mapped_unique_intra_quality_anchor=8283 Thu Nov 8 17:29:21 PST 2018: Mapped_unique_intra_quality_anchor_small=8118 Thu Nov 8 17:29:21 PST 2018: Mapped_unique_intra_quality_anchor_med=74 Thu Nov 8 17:29:21 PST 2018: Mapped_unique_intra_quality_anchor_large=91 Thu Nov 8 17:29:21 PST 2018: Creating UCSC Compatible files; make sure tabix and bgzip are available in the environment or this will not work. Thu Nov 8 17:29:22 PST 2018: Loop_PETs=74 Thu Nov 08 17:29:22 PST 2018: ['/home/groups/oroaklab/src/R/R-3.5.1/bin/Rscript', u'hichipper_CGGTCC/qcReport.R', '/home/groups/oroaklab/src/pyenv/versions/2.7.9/lib/python2.7/site-packages/hichipper', 'hichipper_CGGTCC', '/projects/chip/181106_expt7/analysis/hichipper', '0.7.3', 'RO19.CGGTCC RO18.CGGTCC RO14.CGGTCC'] /projects/chip/181106_expt7/analysis/hichipperUsing count as value column: use value.var to override. Processing: RO19.CGGTCCRO18.CGGTCCRO14.CGGTCC Error in { : task 1 failed - "incorrect number of dimensions" Calls: %do% -> Execution halted

Also, I'm aware that the long-range anchors are minimal in this dataset.

caleblareau commented 6 years ago

Yea, with only 74 Loop PETs, the issue is coming with trying to fit the loop-associated model. The crash, while inelegant, is symptomatic of not having enough data to fit this model. I’d suggest re-running with an expanded anchor set.

On Nov 8, 2018, at 8:36 PM, boconnell89 notifications@github.com wrote:

hichipper consistently crashes at the qcReport step (even with individual libraries). I've pasted the error code below:

Thu Nov 8 17:29:19 PST 2018: Total number of reads in anchors: 2544455 Thu Nov 8 17:29:21 PST 2018: Mapped_unique_intra_quality_anchor=8283 Thu Nov 8 17:29:21 PST 2018: Mapped_unique_intra_quality_anchor_small=8118 Thu Nov 8 17:29:21 PST 2018: Mapped_unique_intra_quality_anchor_med=74 Thu Nov 8 17:29:21 PST 2018: Mapped_unique_intra_quality_anchor_large=91 Thu Nov 8 17:29:21 PST 2018: Creating UCSC Compatible files; make sure tabix and bgzip are available in the environment or this will not work. Thu Nov 8 17:29:22 PST 2018: Loop_PETs=74 Thu Nov 08 17:29:22 PST 2018: ['/home/groups/oroaklab/src/R/R-3.5.1/bin/Rscript', u'hichipper_CGGTCC/qcReport.R', '/home/groups/oroaklab/src/pyenv/versions/2.7.9/lib/python2.7/site-packages/hichipper', 'hichipper_CGGTCC', '/projects/chip/181106_expt7/analysis/hichipper', '0.7.3', 'RO19.CGGTCC RO18.CGGTCC RO14.CGGTCC'] /projects/chip/181106_expt7/analysis/hichipperUsing count as value column: use value.var to override. Processing: RO19.CGGTCCRO18.CGGTCCRO14.CGGTCC Error in { : task 1 failed - "incorrect number of dimensions" Calls: %do% -> Execution halted

Also, I'm aware that the long-range anchors are minimal in this dataset.

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francisfa commented 4 years ago

Hi, I have the similar issue. But, what is the expanded anchor set? Does it mean to call more peaks?