The ice.log reported an error, but my raw matrix had been iced successfully.

[jiangpuxuan]

When I head /ice_1000000.log, it looks like ice encountered an error:

/Array-Tuqiang/pxjiang/miniconda3/envs/hicpro3.1/bin/python /Array-Tuqiang/pxjiang/packages//HiC-Pro_3.1.0/scripts/ice --results_filename hic_results/matrix/SRR14670388/iced/1000000/SRR14670388_1000000_iced.matrix --filter_low_counts_perc 0.02 --filter_high_counts_perc 0 --max_iter 100 --eps 0.1 --remove-all-zeros-loci --output-bias 1 hic_results/matrix//SRR14670388/raw/1000000/SRR14670388_1000000.matrix /Array-Tuqiang/pxjiang/packages//HiC-Pro_3.1.0/scripts/ice:65: SyntaxWarning: "is" with a literal. Did you mean "=="? if "--filtering_perc" is None and "--filter_low_counts_perc" not in sys.argv: /Array-Tuqiang/pxjiang/miniconda3/envs/hicpro3.1/lib/python3.8/site-packages/iced/normalization/_ca_utils.py:8: UserWarning: The API of this module is likely to change. Use only for testing purposes warnings.warn( Assuming the file is 1-based. If this is not the desired option, set option --base to 0

However, it appeared normal in my log for ~/packages/HiC-Pro-master/bin/HiC-Pro, no error was reported :

Logs: logs/SRR12435868/ice_20000.log Logs: logs/SRR12435868/ice_40000.log Logs: logs/SRR12435868/ice_150000.log Logs: logs/SRR12435868/ice_500000.log Logs: logs/SRR12435868/ice_1000000.log Logs: logs/SRR14670388/ice_20000.log Logs: logs/SRR14670388/ice_40000.log Logs: logs/SRR14670388/ice_150000.log Logs: logs/SRR14670388/ice_500000.log Logs: logs/SRR14670388/ice_1000000.log

When I look into my matrix, it seems that they have been iced successfully. Raw:

1 1 112 1 2 28 1 3 2 1 6 2 1 7 5 1 8 2 1 11 2 1 12 2 1 13 1 1 14 1

Iced:

1 1 3910.979146 1 2 841.528309 1 3 64.079865 1 6 84.466665 1 7 151.959959 1 8 63.944928 1 11 93.948140 1 12 69.718344 1 13 60.303662 1 14 40.049700

Very appreciate for your help!

[nservant]

Hi, I think these are just warnings ! Best

[jiangpuxuan]

Hi, I think these are just warnings ! Best

Thank you for your help.