../\scripts//Makefile:194: ice_norm] Error 139

[zhanwen-cheng]

Hi, nservant, many thanks for HiC-Pro. Recently I was runing my data using HiC-Pro with HiC-Pro 2.11.4 in our HPC clusters:

(hic) [iese-chengzw@fat03 ~]$ ~/softwares/hic/HiC-Pro_2.11.4/bin/HiC-Pro -h usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v] Use option -h|--help for more information

HiC-Pro 2.11.4

OPTIONS

-i|--input INPUT : input data folder; Must contains a folder per sample with input files -o|--output OUTPUT : output folder -c|--conf CONFIG : configuration file for Hi-C processing [-p|--parallel] : if specified run HiC-Pro on a cluster [-s|--step ANALYSIS_STEP] : run only a subset of the HiC-Pro workflow; if not specified the complete workflow is run mapping: perform reads alignment - require fast files proc_hic: perform Hi-C filtering - require BAM files quality_checks: run Hi-C quality control plots merge_persample: merge multiple inputs and remove duplicates if specified - require .validPairs files build_contact_maps: Build raw inter/intrachromosomal contact maps - require .allValidPairs files ice_norm : run ICE normalization on contact maps - require .matrix files

Everything went well but a error occuried during ICE normalization like this:

…… Thu Nov 19 15:27:54 Local time zone must be set--see zic manual page 2020 Generate binned matrix files ... Logs: logs/fastp/build_raw_maps.log

---

Thu Nov 19 15:27:58 Local time zone must be set--see zic manual page 2020 Run ICE Normalization ... Logs: logs/fastp/ice_20000.log make: *** [/home/iese-chengzw/softwares/hic/HiC-Pro_2.11.4/bin/../scripts//Makefile:194: ice_norm] Error 139

And in ice_20000.log file, it shows: `ice --results_filename hic_results/matrix/fastp/iced/20000/fastp_20000_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 --verbose 1 hic_results/matrix//fastp/raw/20000/fastp_20000.matrix /home/iese-chengzw/anaconda3/envs/hic/lib/python2.7/site-packages/iced/normalization/_ca_utils.py:9: UserWarning: The API of this module is likely to change. Use only for testing purposes "The API of this module is likely to change. " /home/iese-chengzw/softwares/hic/HiC-Pro_2.11.4/scripts/hic.inc.sh: line 86: 56424 Segmentation fault (core dumped) ice --results_filename hic_results/matrix/fastp/iced/20000/fastp_20000_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 --verbose 1 hic_results/matrix//fastp/raw/20000/fastp_20000.matrix

I checked my iced version, the version and the path was right like below:

(hic) [iese-chengzw@fat03 fastp]$ python Python 2.7.18 |Anaconda, Inc.| (default, Apr 23 2020, 22:42:48) [GCC 7.3.0] on linux2 Type "help", "copyright", "credits" or "license" for more information.

import iced /home/iese-chengzw/anaconda3/envs/hic/lib/python2.7/site-packages/iced/normalization/_ca_utils.py:9: UserWarning: The API of this module is likely to change. Use only for testing purposes "The API of this module is likely to change. " iced.version '0.5.6' iced.path ['/home/iese-chengzw/anaconda3/envs/hic/lib/python2.7/site-packages/iced']

And if I log into my calculating nodes to execute the sgematation fault command, it succeeded:

(hic) [iese-chengzw@fat03 yca30]$ cd result/ (hic) [iese-chengzw@fat03 result]$ ll total 20 drwxr-xr-x 5 iese-chengzw iese-xiayu 4096 Nov 19 22:46 bowtie_results -rwxr-xr-x 1 iese-chengzw iese-xiayu 3025 Nov 19 21:09 config-hicpro.txt drwxr-xr-x 6 iese-chengzw iese-xiayu 4096 Nov 19 23:27 hic_results drwxr-xr-x 3 iese-chengzw iese-xiayu 4096 Nov 19 21:09 logs lrwxrwxrwx 1 iese-chengzw iese-xiayu 36 Nov 19 21:09 rawdata -> /work/iese-chengzw/hic/yca30/rawdata drwxr-xr-x 2 iese-chengzw iese-xiayu 4096 Nov 19 21:09 tmp (hic) [iese-chengzw@fat03 result]$ ice --results_filename hic_results/matrix/fastp/iced/20000/fastp_20000_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 --verbose 1 hic_results/matrix//fastp/raw/20000/fastp_20000.matrix /home/iese-chengzw/anaconda3/envs/hic/lib/python2.7/site-packages/iced/normalization/_ca_utils.py:9: UserWarning: The API of this module is likely to change. Use only for testing purposes "The API of this module is likely to change. " Using iced version 0.5.6 Loading files... Normalizing... Filter 212661 out of 215355 bins ... Matrix is triangular superior Writing results...

I think the iced pacakage is alright but can't be called if I run it in complete workflow. The attachments are my .PBS file and my config-hicpro.txt. Can you help me to fix that? config-hicpro.txt hic_yca30.pbs.txt.txt

[zhanwen-cheng]

I noticed that under matirx raw path, there are 20000/40000/500000/1000000 file, but under matrix iced path, only exits 20000 file. Considering I only haven't finished iced normalization, can I just finish the left step but '-s ice_norm' with my 'matrix' file as input? Would there be some differences between this way and complete work flow?

[nservant]

Hi, It's not clear to me why iced crashed, but yes you can run the normalization only using -s ice_norm. Note that in this case, the input folder should contains the matrix files (and no longer the fastq files). Let me know if you have any other trouble best

[zhanwen-cheng]

OK, IC. Thanks~