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4dn-dcic / hic2cool

Lightweight converter between hic and cool contact matrices.
MIT License
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Error -3 while decompressing data #45

Closed chenggang108 closed 4 years ago

chenggang108 commented 4 years ago

Hi I am trying to convert .hic file to mcool. It show error. Here is how it looks. Header info from hic ... Chromosomes: ['ALL', '1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '3', '4', '5' , '6', '7', '8', '9', 'M', 'X', 'Y'] ... Resolutions: [2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000] ... Normalizations: ['VC', 'VC_SQRT', 'KR'] ... Genome: /usr/local/apps/hicpro/2.11.1/annotation/chrom_mm10.sizes

Converting

... Resolution 2500000 took: 18.117652416229248 seconds. ... Resolution 1000000 took: 13.354706525802612 seconds. ... Resolution 500000 took: 48.48037791252136 seconds. ... Resolution 250000 took: 139.53048062324524 seconds. multiprocessing.pool.RemoteTraceback: "" Traceback (most recent call last): File "/data/chengg2/conda/envs/hic2cool/lib/python3.6/multiprocessing/pool. py", line 119, in worker result = (True, func(*args, **kwds)) File "/data/chengg2/conda/envs/hic2cool/lib/python3.6/site-packages/hic2coo l/hic2cool_utils.py", line 379, in build_counts_chunk records = read_block(req, block_record) File "/data/chengg2/conda/envs/hic2cool/lib/python3.6/site-packages/hic2coo l/hic2cool_utils.py", line 232, in read_block uncompressedBytes = zlib.decompress(compressedBytes) zlib.error: Error -3 while decompressing data: too many length or distance sy mbols """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/data/chengg2/conda/envs/hic2cool/bin/hic2cool", line 8, in sys.exit(main()) File "/data/chengg2/conda/envs/hic2cool/lib/python3.6/site-packages/hic2coo l/main.py", line 86, in main hic2cool_convert(args.infile, args.outfile, args.resolution, args.nproc, args.warnings, args.silent) File "/data/chengg2/conda/envs/hic2cool/lib/python3.6/site-packages/hic2coo l/hic2cool_utils.py", line 940, in hic2cool_convert used_chrs, show_warnings) File "/data/chengg2/conda/envs/hic2cool/lib/python3.6/site-packages/hic2coo l/hic2cool_utils.py", line 361, in parse_hic result_all.extend(mpi_result[mpi].get()) File "/data/chengg2/conda/envs/hic2cool/lib/python3.6/multiprocessing/pool. py", line 644, in get raise self._value zlib.error: Error -3 while decompressing data: too many length or distance sy mbols

SooLee commented 4 years ago

Have you checked the hic file is correct and not corrupt?

chenggang108 commented 4 years ago

Hi Lee,

The .hic file shows perfect matrix in juicebox.

SooLee commented 4 years ago

Are you using multi-processing?

chenggang108 commented 4 years ago

That's something I am trying now. It looks going further. Thank you for your answer. I will let you know

SooLee commented 4 years ago

@chenggang108 How did it go?

chenggang108 commented 4 years ago

@SooLee Sorry for the delay. Multi-processing works

SooLee commented 4 years ago

Great. Thanks!