Closed genferreri closed 4 years ago
Hello Lucas @genferreri, thanks very much for using SNPGenie. Unfortunately, this is not a problem I can diagnose without seeing your input file. Please provide a link to an example of your problematic input and I'll check it out. Some likely sources of error are that the file is not tab-delimited, or is using Windows CRLF (\r\n) or Mac line endings instead of Unix (\n) (see Troubleshooting).
Hello Chase, thanks for the prompt answer. I went through troubleshooting and I made sure that is tab-delimited and has Unix line endings (In sublime). You can find the vcf file along with reference and gtf file here. I uploaded the last two just in case the problem does not come from the vcf (?). Sorry for the troubles. Thanks Lucas
Thanks. Please also provide the command you used, including all arguments, so I can duplicate the conditions under which the error occurred. Then I'll be able to take a look.
This is the line: perl snpgenie.pl --minfreq=0.02 --vcfformat=4 --snpreport=AO-256_cutadapt_LoFreq.clean.vcf --fastafile=WF10_continuous-RF.fa --gtffile=WF10_continuous.gtf.txt
Dear @genferreri : apologies, as I have just moved to another country and quite lost track of my 'to-do' list.
Your VCF file is not vcfformat 4, it is vcfformat 2 (see SNPGenie's documentation). It works for me (and the output makes sense, at first glance) when specifying the correct input:
snpgenie.pl --minfreq=0.02 --vcfformat=2 --snpreport=AO-256_cutadapt_LoFreq.vcf --fastafile=WF10_continuous-ORF.fa --gtffile=WF10_continuous.gtf.txt
Here are the results I obtain. Let me know.
Yours, Chase
Hello @cwnelson88 , no worries, I moved myself from country several times, I know the stress. I am glad that the problem was rather simple to solve. Although I am a little confused since the header of the vcf file specifies "##fileformat=VCFv4.0". I will run this in my computer and I will let you know wether it worked or not. Thank you very much again.
Lucas
Hello Chase, I am trying to run SNPGenie and I got the following error: temp_vcf4_POS.vcf does not contain the standard VCF column header "ID". SNPGenie terminated. I checked the .vcf file (produced by LoFreq) and the "ID" header is there and it is also present in the temp_vcf4_ID.vcf file. So up to that point the program is able to parse the "ID" column. I am not sure what can be wrong. I hope you can help me.
Thanks
Lucas