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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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_expected.pkl is not found #10

Closed Bo-UT closed 2 years ago

Bo-UT commented 2 years ago

Hi Xiaotao,

Thanks for all your help! Sorry to bother you again, but I got another error saying ".231043-HC01_5000.mcool.175822081.CNV.None.100000.None/chr4_expected.pkl". I listed the directory .231043-HC01_5000.mcool.175822081.CNV.None.100000.None, but I do see 'chr4_expected.pkl' is there. Not sure what's the problem there. Thanks.

Bo

FileNotFoundError: [Errno 2] No such file or directory: '.231043-HC01_5000.mcool.175822081.CNV.None.100000.None/chr4_expected.pkl' Traceback (most recent call last): File "/rsrch4/home/genomic_med/bzhao2/miniconda3/envs/EagleC/bin/predictSV", line 176, in run() File "/rsrch4/home/genomic_med/bzhao2/miniconda3/envs/EagleC/bin/predictSV", line 159, in run subprocess.check_call(' '.join(command), shell=True) File "/rsrch4/home/genomic_med/bzhao2/miniconda3/envs/EagleC/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'merge-multiple-resolutions --hic-10k ../CatalystHiCmcool/231045-HC01_5000.mcool::resolutions/10000 --hic-5k ../CatalystHiCmcool/231045-HC01_5000.mcool::resolutions/5000 --balance-type CNV -C "#" "X" --full-sv-files 231045-HC01_5000.CNN_SVs.5K.txt 231045-HC01_5000.CNN_SVs.10K_highres.txt 231045-HC01_5000.CNN_SVs.50K_highres.txt -O 231045-HC01_5000.CNN_SVs.5K_combined.txt --buff-size 50000 --output-format NeoLoopFinder --cache-10k .231043-HC01_5000.mcool.175822081.CNV.None.100000.None --cache-5k .235206-HC01_5000.mcool.131736076.CNV.None.100000.None' returned non-zero exit status 1.

XiaoTaoWang commented 2 years ago

Hi Bo,

I think this error was caused by a bug in predictSV, because predictSV extracts the --cache-10k and --cache-5k from your log file, and if you ran predictSV with the same --logFile setting on multiple samples, this function can result in conflicts. That's why in your log, the prefixes of --cache-10k and --cache-5k are different from your cool files.

I have fixed this by removing the --logFile parameter in the new version (v0.1.7), and now the log file name will use the prefix determined by --output-prefix as well. Can you try this new version and let me know if it works (you may need to rerun EagleC in a fresh new folder)? Thanks!

Xiaotao

Bo-UT commented 2 years ago

sure thing! Will let you know how it works. Thanks

Bo

Bo-UT commented 2 years ago

Hi Xiaotao,

Wanted to let you know that V0.1.7 EagleC works. So far one third of my jobs have been successfully done. Thanks a lot for your help!

Best, Bo

XiaoTaoWang commented 2 years ago

Great! Thanks for letting me know.

Xiaotao