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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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build_raw_maps error #368

Closed shiyi-pan closed 3 years ago

shiyi-pan commented 4 years ago

hi, I run HiC-Pro in test data and it run well but when I used it on my data , I met a error like this:

Mon Sep 21 14:58:24 CST 2020 Pairing of R1 and R2 tags ... Logs: logs/sample1/mergeSAM.log

Mon Sep 21 19:48:08 CST 2020 Assign alignments to restriction fragments ... Logs: logs/sample1/mapped_2hic_fragments.log

Tue Sep 22 03:19:53 CST 2020 Merge chunks from the same sample ... Logs: logs/sample1/merge_valid_interactions.log

Tue Sep 22 03:24:08 CST 2020 Merge stat files per sample ... Logs: logs/sample1/merge_stats.log

Tue Sep 22 03:24:09 CST 2020 Run quality checks for all samples ... Logs: logs/sample1/make_Rplots.log

Tue Sep 22 03:24:32 CST 2020 Generate binned matrix files ... Logs: logs/sample1/build_raw_maps.log make: *** [build_raw_maps] Error 134

I tracked the error and found the logs when it happended. here is the logs:

cat hic_results/data//sample1/sample1.allValidPairs | /ds3512/home/panyp/ruanjian/hic-pro/HiC-Pro_2.11.1/scripts/build_matrix --matrix-format upper --binsize 500000 --chrsizes /ds3512/home/panyp/ru anjian/hic-pro/HiC-Pro_2.11.1/annotation/genome.fasta.size --ifile /dev/stdin --oprefix hicresults/matrix/sample1/raw/500000/sample1${bsize} build_matrix: /ds3512/home/panyp/Hi-C/HiC-Pro-2.11.1/scripts/src/build_matrix.cpp:225: Chromosome::Chromosome(const std::string&, chrsize_t, chrsize_t, chrsize_t, bool, const ChrRegions*): Assertio n `chr_map.find(name) == chr_map.end()' failed. /ds3512/home/panyp/ruanjian/hic-pro/HiC-Pro_2.11.1/scripts/hic.inc.sh: line 86: 3404 Broken pipe cat hic_results/data//sample1/sample1.allValidPairs 3405 Aborted | /ds3512/home/panyp/ruanjian/hic-pro/HiC-Pro_2.11.1/scripts/build_matrix --matrix-format upper --binsize 500000 --chrsizes /ds3512/home/panyp/ruanjian/hic-pro/Hi C-Pro_2.11.1/annotation/genome.fasta.size --ifile /dev/stdin --oprefix hicresults/matrix/sample1/raw/500000/sample1${bsize}

could you give me some advise ? Thank you very much.

nservant commented 4 years ago

Hi Could you first check that the allvalidPairs file in data is not empty ? Thanks

shiyi-pan commented 4 years ago

Hi，thank you for your response, the sample1.allValidPairs in data file is 6Gb.

nservant commented 4 years ago

hum... could you check if the list of chromosmes in the file /ds3512/home/panyp/ruanjian/hic-pro/HiC-Pro_2.11.1/annotation/genome.fasta.size correspond to the one you have in the allValidPairs one please ?

shiyi-pan commented 4 years ago

Thank you for your reply,they are not correspond . Maybe this is the problem . I will correct it and try again . Thank you again for your help.

nservant commented 4 years ago

Yes. HiC-Pro builds the maps for the chromosomes which are in the chromosome.size file