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thomasvangurp / epiGBS

Code for working with epiGBS data
MIT License
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map_STAR.py : command not found #7

Open justinjohns opened 7 years ago

justinjohns commented 7 years ago

I think that make_reference ran successfully (although it claims a 'fatal error: unable to reallocate enough memory' near the end of the log), however I am having trouble getting mapping_variant_calling.py to run.

I attached the make_reference.log in case this is where things got off track. make_reference.txt

Here is the command: jus@jus:~/SEQ/epiGBS/mapping_varcall$ python mapping_variant_calling.py --tmpdir /tmp/ --input_dir /media/jus/seq/epiGBS_Demul_Output/denovo/ --barcodes ./barcodes.csv --threads 3 --output_dir /media/jus/seq/epiGBS_Demul_Output/output_mapping/

and the error:

Traceback (most recent call last): File "mapping_variant_calling.py", line 620, in main() File "mapping_variant_calling.py", line 612, in main files = run_STAR(files,args)

File "mapping_variant_calling.py", line 235, in run_STAR run_subprocess(cmd, args, log) File "mapping_variant_calling.py", line 108, in run_subprocess raise RuntimeError(stderr) RuntimeError: /bin/bash: map_STAR.py: command not found

Running $ python map_STAR.py returns: SyntaxError: Non-ASCII character '\xe2' in file map_STAR.py on line 334, but no encoding declared; see http://python.org/dev/peps/pep-0263/ for details

and line 334 in map_STAR.py is:

outFilterScoreMinOverLread : float: same as outFilterMatchNmin, but normalized to the read length (sum of mates’ lengths for paired-end reads)

justinjohns commented 7 years ago

map_STAR.py ran after deleting the comment lines 334-337, and placing all relevant in /usr/local/bin with full permissions and changing the shebang to #! /usr/bin/python2.7.

Additional required dependencies: pip install PyVCF \ pip install HTSeq \ sudo apt install rna-star \ sudo apt-get install tabix

mapping_variant_calling.py ran for 12 hours, and ran into an arguments error "now starting: ['Run methylation calling script'] running: methylation_calling.py -r /media/jus/seq/refout6/consensus_cluster.renamed.fa -m /media/jus/seq/variant5/merged.tsv.gz -s /media/jus/seq/variant5/snp.vcf.gz -o /media/jus/seq/variant5/methylation.bed -heat /media/jus/seq/variant5/heatmap.igv stderr: usage: methylation_calling.py [-h] [-r [REFERENCE]] [-w [WATSON]] [-c [CRICK]] [-m [METHYLATION_OUTPUT]] [-s [SNP_OUTPUT]] [-heat [HEATMAP_OUTPUT]] [-methylation_called [METHYLATION_CALLED]] [-snp_called [SNP_CALLED]] [-qual [MIN_QUALITY]] methylation_calling.py: error: unrecognized arguments: -o /media/jus/seq/variant5/methylation.bed"

I changed the -o in mapping_variant_calling.py to an -m, but now am running into this issue:

"now starting: ['Run methylation calling script'] running: methylation_calling.py -r /media/jus/seq/refout6/consensus_cluster.renamed.fa -m /media/jus/seq/variant6/merged.tsv.gz -s /media/jus/seq/variant6/snp.vcf.gz -m /media/jus/seq/variant6/methylation.bed -heat /media/jus/seq/variant6/heatmap.igv stderr: Traceback (most recent call last): File "/usr/local/bin/methylation_calling.py", line 889, in main() File "/usr/local/bin/methylation_calling.py", line 47, in main files = parse_vcf(args) File "/usr/local/bin/methylation_calling.py", line 69, in parse_vcf methyl_called_file = open(args.methylation_called, 'w') TypeError: coercing to Unicode: need string or buffer, NoneType found" mapping_variantcalling.txt