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yupenghe / methylpy

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
Apache License 2.0
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error in mapping. #21

Closed CS791 closed 5 years ago

CS791 commented 5 years ago

Hi! yupenghe,

I am using methylpy first time and I am not very good in computer programming. Any help will be much appreciated.

I am trying to map my paired-end reads to transposable elements of Arabidopsis with the following command line: methylpy paired-end-pipeline --read1-files New_Analysis/Data/Epiril368_4_C_R1_L001_R1.fastq.gz --read2-files New_Analysis/Data/Epiril368_4_C_R1_L001_R2.fastq.gz --sample New_Analysis/New_Output/TE/epiRIL368_4°C_Rep1_Lane1_TE --forward-ref New_Analysis/TE_Genome/TAIR10_TE_f --reverse-ref New_Analysis/TE_Genome/TAIR10_TE_r --ref-fasta New_Analysis/TE_Genome/TAIR10_TE.fas --generate-allc-file True --num-procs 4 --compress-output True --remove-clonal True --path-to-picard="picard/" But with alignment I got the following warnings:

Traceback (most recent call last): File "/home/saurabh/anaconda3/bin/methylpy", line 4, in import('pkg_resources').run_script('methylpy==1.3.4', 'methylpy') File "/home/saurabh/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 664, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/saurabh/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 1444, in run_script exec(code, namespace, namespace) File "/home/saurabh/anaconda3/lib/python3.6/site-packages/methylpy-1.3.4-py3.6.egg/EGG-INFO/scripts/methylpy", line 5, in parse_args() File "/home/saurabh/anaconda3/lib/python3.6/site-packages/methylpy-1.3.4-py3.6.egg/methylpy/parser.py", line 185, in parse_args keep_temp_files=args.keep_temp_files) File "/home/saurabh/anaconda3/lib/python3.6/site-packages/methylpy-1.3.4-py3.6.egg/methylpy/call_mc_pe.py", line 342, in run_methylation_pipeline_pe keep_temp_files=keep_temp_files) File "/home/saurabh/anaconda3/lib/python3.6/site-packages/methylpy-1.3.4-py3.6.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe path_to_samtools=path_to_samtools) File "/home/saurabh/anaconda3/lib/python3.6/site-packages/methylpy-1.3.4-py3.6.egg/methylpy/call_mc_pe.py", line 1265, in flip_read2_strand for line in input_pipe.stdout: File "/home/saurabh/anaconda3/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb0 in position 509: invalid start byte

I don't understand exactly what it is.

Thank you! Regards CS791

yupenghe commented 5 years ago

Hey CS791, Is this error reproducible? If you run your command again, will you get the same error?

Yupeng

CS791 commented 5 years ago

Hello! Yupeng,

Thank you! for your reply. Yes! it does reproducible and I got the same error when I run with same input as well as other input files.

Thank you. Regards

CS791

yupenghe commented 5 years ago

Ok. If you use python2 instead of python3, would you still see this problem? This may be the quickest fix.

What output/intermediate files were generated when you ran methylpy? What are their sizes? Would it be possible for you to share some input files for me to reproduce this error? Thanks.

CS791 commented 5 years ago

Thanks again. I will try with python2 instead of python3, and let you know. As far as output files are concerned, surprisingly I got only two bam files of sizes around 216 MB. That might be possible as my reference is only transposable element genes, not the whole genome. But I am not able to generate allc files. Thank you! for suggestions. I will let you know once I will do with python2