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vaquerizaslab / chess

Comparison of Hi-C Experiments using Structural Similarity.
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Error when running CHESS on JUICER HIC files #38

Open rkuzya opened 3 years ago

rkuzya commented 3 years ago

Hello,

I would highly appreciate your help with the issues I have been facing when trying to run CHESS on my HIC files.

I have installed CHESS (0.3.6) and successfully tested it on the data provided in the repository. All output files and plots (for CHESS data sets) have been generated by following the instructions provided in the online manual and the jupyter notebook.

Unfortunately, the tool has crashed when new data (Juicer HIC files) had been provided. Here is the CHESS error message for the command I have used:

chess sim -p 6 CTRL_1.hic ./Tip5_1.hic mm10_chr2_3mb_win_100kb_step.bed ./chr2.result 2021-02-11 12:36:01,017 INFO CHESS version: 0.3.6 2021-02-11 12:36:01,018 INFO FAN-C version: 0.9.10 2021-02-11 12:36:01,019 INFO Loading reference contact data 2021-02-11 12:37:47,218 INFO Loading query contact data 2021-02-11 12:39:05,585 INFO Loading region pairs 2021-02-11 12:39:05,589 WARNING 2392 region pairs have been dropped, because they involve chromosomes that are not present in the provided contact data. 2021-02-11 12:39:05,589 ERROR No valid region pairs found; aborting.

I have been working with MM10 genome and the hic files have been produced with Juicer. Here is the validation of the HIC files done with the Juicer tools:

TIP5_1 juicer tool validation: Reading file: ./Tip5_1.hic File has normalization: VC Description: Coverage File has normalization: VC_SQRT Description: Coverage (Sqrt) File has normalization: KR Description: Balanced File has zoom: BP_2500000 File has zoom: BP_1000000 File has zoom: BP_500000 File has zoom: BP_250000 File has zoom: BP_100000 File has zoom: BP_50000 File has zoom: BP_25000 File has zoom: BP_10000 File has zoom: BP_5000

CTRL_1 validation: Reading file: ./CTRL_1.hic File has normalization: VC Description: Coverage File has normalization: VC_SQRT Description: Coverage (Sqrt) File has normalization: KR Description: Balanced File has zoom: BP_2500000 File has zoom: BP_1000000 File has zoom: BP_500000 File has zoom: BP_250000 File has zoom: BP_100000 File has zoom: BP_50000 File has zoom: BP_25000 File has zoom: BP_10000 File has zoom: BP_5000

Any help on the current issue would be highly appreciated. With best regards. Ross

kaukrise commented 3 years ago

Please have a look here, to see if it solves your issue: #36

rkuzya commented 3 years ago

Thank you very much for your help! It worked. I got the output file. As in issue #36, I also got a message: Could not compute similarity for 68 region pairs. This can be due to faulty coordinates, too small region sizes or too many unmappable bins

But it is ok.
I will proceed with further analysis as indicated in the manual and contact you when having some questions.

Best. Ross