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XiaoTaoWang / EagleC

A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
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predictSV have some error #11

Closed yangfeizZZ closed 2 years ago

yangfeizZZ commented 2 years ago

when i run predictSV,i have some error. My code: predictSV --hic-5k M1.mcool::/resolutions/5000 --hic-10k M1.mcool::/resolutions/10000 --hic-50k M1.mcool::/resolutions/50000 -O SK-N-AS -g hg38 --balance-type ICE --output-format NeoLoopFinder --prob-cutoff-5k 0.8 --prob-cutoff-10k 0.8 --prob-cutoff-50k 0.99999 My error:File "/home/marh/miniconda3/envs/EagleC/bin/predictSV-single-resolution", line 276, in run() File "/home/marh/miniconda3/envs/EagleC/bin/predictSV-single-resolution", line 227, in run intra_expected_count = intraPredict(clr, cnn_models, chroms, cache_folder, seq_depth, File "eaglec/scoreUtils.pyx", line 1263, in eaglec.scoreUtils.intraPredict File "eaglec/scoreUtils.pyx", line 1022, in eaglec.scoreUtils._intra_global_core File "/home/marh/miniconda3/envs/EagleC/lib/python3.8/site-packages/eaglec/utilities.py", line 380, in check_gaps_and_decays gaps = load_gap(clr, ref_genome=ref, balance=balance) File "/home/marh/miniconda3/envs/EagleC/lib/python3.8/site-packages/eaglec/utilities.py", line 326, in load_gap if ref_gaps[chromlabel][ref_i]: IndexError: index 24896 is out of bounds for axis 0 with size 24896 Traceback (most recent call last): File "/home/marh/miniconda3/envs/EagleC/bin/predictSV", line 176, in run() File "/home/marh/miniconda3/envs/EagleC/bin/predictSV", line 112, in run subprocess.check_call(' '.join(command), shell=True) File "/home/marh/miniconda3/envs/EagleC/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'predictSV-single-resolution -H M1.mcool::/resolutions/5000 --balance-type ICE -O SK-N-AS.CNN_SVs.5K.txt --genome hg38 --output-format full -C "#" "X" --prob-cutoff 0.8 --logFile SK-N-AS.log' returned non-zero exit status 1. How to solve it,thanks you.

XiaoTaoWang commented 2 years ago

Hi, the error tells that your Hi-C reads were not mapped to the reference genome you specified in command (-g hg38). Can you double check the reference genome you used for mapping?

yangfeizZZ commented 2 years ago

Hi, the error tells that your Hi-C reads were not mapped to the reference genome you specified in command (-g hg38). Can you double check the reference genome you used for mapping?

YES,when i change hg19,it irun successfully.