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WGLab / RepeatHMM

a hidden Markov model to infer simple repeats from genome sequences
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Multi-thread errors #42

Open woodoo46 opened 3 years ago

woodoo46 commented 3 years ago

Hi,

When I ran repeatHMM with multi-threaded mode, for example with option --thread 8. I had this error

lib/python2.7/site-packages/RepeatHMM-2.0-py2.7-linux-x86_64.egg/RepeatHMM_scripts/myScanWholeGenome.py", line 466, in scan_part ti, mi, chrk = curPartition[-1] ValueError: too many values to unpack

This is my command: ${repeatHMM} Scan --SplitAndReAlign 1 --MinSup 3 --UserDefinedUniqID chr10.0000.scan --SeqTech Pacbio --Patternfile ${patternfile} --Onebamfile ${bamfile} --hgfile ${genome} --thread 8 --cluster 0

If I do not set --thread, the program went through.

Thanks!.

George

liuqianhn commented 3 years ago

@woodoo46 Thanks for reporting this issue and for being interested in scan module. I will check it and fix the issue.

LiShuhang-gif commented 3 years ago

Hi, have you already fix this issue? I have encountered the same "ValueError" when using multiple threads.

shaohua-fan commented 3 years ago

@liuqianhn we met the same problem when using the scan module with multi-thread mode.

We used

repeatHMM.py Scan --SplitAndReAlign 1 --MinSup 3 --UserDefinedUniqID WGSscan --SeqTech "Nanopore" "--Patternfile" hg38.trf.bed --cluster 0 --envset repeathmmenv --Onebamfile minimap2_sorted_rmdup_p20.bam --hgfile hg38_22_XYM.fa --thread 10

We observed the followings error messages:

Process Process-1: Traceback (most recent call last): File "/public/home/yes/envs/repeathmmenv/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/public/home/yes/envs/repeathmmenv/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/public/home/repeatHMM/RepeatHMM/bin/RepeatHMM_scripts/myScanWholeGenome.py", line 466, in scan_part ti, mi, chrk = curPartition[-1] ValueError: too many values to unpack

Can you please let us know how to fix this problem?

genkiguan commented 2 years ago

@liuqianhn Hi, I also met the same problem when using multi-thread. Could you please help me figure it out?

quantrannnn commented 8 months ago

@liuqianhn Hi, I met the same error when running repeatHMM Scan in multi-thread mode. I only can run with --thread 1 but it took too much time. Could you help me with this problem? Thanks