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waterlandlab / CluBCpG

Cluster-based analysis of CpG methylation
https://clubcpg.readthedocs.io/
MIT License
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Invalid literal error when running clubcpg-cluster #16

Closed DLGisch closed 2 years ago

DLGisch commented 2 years ago

Hello,

When I try to run clubcpg-cluster -a ../../d/Bismark_hg38/bam/small.bam -o /mnt/f/clubCpG --bins /mnt/f/clubCpG/CompleteBins.small.bam.chr16.log

I get the following error:

Only one input bam detected. Running in single-file mode multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/dgisch/anaconda3/envs/clubCpG/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/home/dgisch/anaconda3/envs/clubCpG/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/dgisch/anaconda3/envs/clubCpG/lib/python3.7/site-packages/clubcpg/ClusterReads.py", line 213, in process_bins bin_loc = int(bin_loc) ValueError: invalid literal for int() with base 10: 'size=100' """

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

Traceback (most recent call last): File "/home/dgisch/anaconda3/envs/clubCpG/bin/clubcpg-cluster", line 147, in cluster_reads.execute() File "/home/dgisch/anaconda3/envs/clubCpG/lib/python3.7/site-packages/clubcpg/ClusterReads.py", line 344, in execute results = results.get() File "/home/dgisch/anaconda3/envs/clubCpG/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value ValueError: invalid literal for int() with base 10: 'size=100'

I am running in an Ubuntu inside a Windows Subsystem Linux, with Python 3.7.

Thank you!

canthonyscott commented 2 years ago

Hello, it looks like you are passing a .log files to the --bins argument. Can you share the contents of that file?

DLGisch commented 2 years ago

The contents of .log file is

INFO:root:Namespace(bin_size=100, chromosome='chr16', input_bam_A='../../d/Bismark_hg38/bam/small.bam', no_overlap=True, num_processors='5', output_dir='/mnt/f/clubCpG', read1_3=0, read1_5=0, read2_3=0, read2_5=0) INFO:root:Input file: ../../d/Bismark_hg38/bam/small.bam INFO:root:Chromosome specified: chr16 INFO:root:Bin size: 100 INFO:root:Number of processors: 5 INFO:root:Fix overlapping reads: True INFO:root:M bias inputs ignoring the following: read 1 5': 0bp read1 3': 0bp read2 5: 0bp read2 3': 0bp INFO:root:Tasks remaining = 903400 INFO:root:Tasks remaining = 903400 INFO:root:Correction attempt at bin chr16_1178200: FAILED INFO:root:Correction attempt at bin chr16_1186100: FAILED INFO:root:Correction attempt at bin chr16_1205000: FAILED INFO:root:Tasks remaining = 903400 INFO:root:Correction attempt at bin chr16_17274100: FAILED INFO:root:Correction attempt at bin chr16_17295500: FAILED INFO:root:Correction attempt at bin chr16_17327600: FAILED INFO:root:Correction attempt at bin chr16_17345900: FAILED INFO:root:Correction attempt at bin chr16_11979300: FAILED INFO:root:Tasks remaining = 903400 INFO:root:Tasks remaining = 858230 INFO:root:Correction attempt at bin chr16_2034600: FAILED INFO:root:Tasks remaining = 813060 INFO:root:Correction attempt at bin chr16_21637100: FAILED INFO:root:Correction attempt at bin chr16_21955000: FAILED INFO:root:Tasks remaining = 813060 INFO:root:Tasks remaining = 767890 INFO:root:Tasks remaining = 722720 INFO:root:Tasks remaining = 677550 INFO:root:Tasks remaining = 632380 INFO:root:Tasks remaining = 542040 INFO:root:Correction attempt at bin chr16_50579600: FAILED INFO:root:Tasks remaining = 451700 INFO:root:Tasks remaining = 451700 INFO:root:Tasks remaining = 451700 INFO:root:Tasks remaining = 361360 INFO:root:Correction attempt at bin chr16_57092500: FAILED INFO:root:Tasks remaining = 361360 INFO:root:Correction attempt at bin chr16_74408300: FAILED INFO:root:Correction attempt at bin chr16_74415800: FAILED INFO:root:Correction attempt at bin chr16_74417600: FAILED INFO:root:Correction attempt at bin chr16_74420500: FAILED INFO:root:Tasks remaining = 271020 INFO:root:Correction attempt at bin chr16_69956300: FAILED INFO:root:Correction attempt at bin chr16_69957200: FAILED

canthonyscott commented 2 years ago

Sorry for the late reply. But you appear to be passing the wrong file to the --bins argument. You are passing the log file being generated not the bins file. Please see this section https://clubcpg.readthedocs.io/en/latest/usage.html#calculate-bin-coverage

DLGisch commented 2 years ago

Sorry my delay to answer too. Thanks, in the example I actually changed the .csv file to .log. I also had a problem because the format of the chromosome name was wrong. I thought it was chr16 and it was actually 16. Thank you for help me