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Error re-running a failed run #41
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Hi Laloverdin,
Issue 1: You're right, your use of the --output dir should be picking up on the coverage files created in the prior degnorm run, but it's not.
Is it just creating a new degnorm_MMDDYY_HMS directory within the output directory you've specified? If yes, this is a bug in utils.py. I can try to look into a fix this weekend.
Issue 2: Regarding the memory error - Degnorm was developed on studies using 6 - 15 RNASeq samples. 60 is a big job (> 60Gb just in raw reads I'm guessing). I would recommend trying the recently developed R package developed by Dr. Wang here: https://github.com/jipingw/DegNorm. It's supposed to be faster and more memory efficient. That, consider a bigger
node, or use fewer samples.
Thanks,
Frank
…On Mon, May 18, 2020 at 4:20 AM laloverdin ***@***.***> wrote:
THe error of the first run is:
File
"/home/isaias.hernandez/anaconda2/envs/degnorm/lib/python3.6/multiprocessing/pool.py",
line 119, in worker
result = (True, func(*args, **kwds))
File
"/home/isaias.hernandez/anaconda2/envs/degnorm/lib/python3.6/site-packages/joblib/_parallel_backends.py",
line 561, in *call*
return self.func(*args, **kwargs)
File
"/home/isaias.hernandez/anaconda2/envs/degnorm/lib/python3.6/site-packages/joblib/parallel.py",
line 261, in *call*
for func, args, kwargs in self.items]
File
"/home/isaias.hernandez/anaconda2/envs/degnorm/lib/python3.6/site-packages/joblib/parallel.py",
line 261, in
for func, args, kwargs in self.items]
File
"/home/isaias.hernandez/anaconda2/envs/degnorm/lib/python3.6/site-packages/DegNorm-0.1.4-py3.6.egg/degnorm/reads_coverage_merge.py",
line 331, in merge_chrom_coverage
cov_mat = cov_mat.asfptype().todense()
File
"/home/isaias.hernandez/anaconda2/envs/degnorm/lib/python3.6/site-packages/scipy/sparse/base.py",
line 721, in todense
return np.asmatrix(self.toarray(order=order, out=out))
File
"/home/isaias.hernandez/anaconda2/envs/degnorm/lib/python3.6/site-packages/scipy/sparse/compressed.py",
line 964, in toarray
return self.tocoo(copy=False).toarray(order=order, out=out)
File
"/home/isaias.hernandez/anaconda2/envs/degnorm/lib/python3.6/site-packages/scipy/sparse/coo.py",
line 252, in toarray
return np.zeros(self.shape, dtype=self.dtype, order=order)
MemoryError
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@ffineis Thanks for the answer, I've already solved issue 1. Regarding to Issue2, I tried the R package and indeed it is faster but it throws me some error when loading some samples, sometimes it charges a samples and sometimes it does not causing the program to be killed before time (read_coverage_batch). Thanks in advance |
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HI, I am trying to pick up a run that failed after calculating the coverage for all my samples but when i re-run the pipeline it creates a new output directory instead of detecting the previous one, maybe i am not inputing correctly the command.
First command (where it failed)
degnorm --bam-dir /media/isaias.hernandez/seagate_ICM/FFPE_PCNSL_98n/STAR_bams -g /media/isaias.hernandez/seagate_ICM/FFPE_PCNSL_98n/FF_vs_FFPE/CNV/CASPER/degnorm/Homo_sapiens.GRCh38.97.gtf -o /media/isaias.hernandez/seagate_ICM/FFPE_PCNSL_98n/degnorm/degnorm_05122020_194420 -p 10
New command to pick up from previously:
degnorm --bam-dir /media/isaias.hernandez/seagate_ICM/FFPE_PCNSL_98n/STAR_bams -g /media/isaias.hernandez/seagate_ICM/FFPE_PCNSL_98n/FF_vs_FFPE/CNV/CASPER/degnorm/Homo_sapiens.GRCh38.97.gtf -o /media/isaias.hernandez/seagate_ICM/FFPE_PCNSL_98n/degnorm/degnorm_05122020_194420
Thanks in advance
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