vcf_to_ima.py error

[xwang111]

Hello, I got the following error when converting data formats. command line: vcf_to_ima.py --vcfs chr01_4gt/chr01_4gt_Chr01-797055-798759.vcf chr01_4gt/chr01_4gt_Chr01-819732-821385.vcf chr01_4gt/chr01_4gt_Chr01-911114-911172.vcf chr01_4gt/chr01_4gt_Chr01-953191-971522.vcf chr01_4gt/chr01_4gt_Chr01-1106335-1157414.vcf --out chr01_ima3_5 --model-file out.model

Traceback (most recent call last): File "/home/miniconda3/envs/py-popgen/bin/vcf_to_ima.py", line 697, in vcf_to_ima(**parseArguments()) File "/home/miniconda3/envs/py-popgen/bin/vcf_to_ima.py", line 675, in vcf_to_ima raise Exception("Individual %d from pop %s at loci %d, site %d is missing data" % (indiv_idx,p,record_count,i)) Exception: Individual 4 from pop T.ciliata_var_ciliata at loci 1, site 0 is missing data

What could I do with my data, please?

[arunsethuraman]

Can you please share a sample input file (VCF) and model file (out.model)? This looks like some formatting error in either of those.

[xwang111]

Dear Sethuraman,

This is the input file (VCF) and model file (out.model), please see if there is anything wrong with it. 

Thank you！ Xi Wang

------------------ 原始邮件 ------------------ 发件人: "jaredgk/PPP" @.>; 发送时间: 2022年7月8日(星期五) 晚上11:58 @.>; @.**@.>; 主题: Re: [jaredgk/PPP] vcf_to_ima.py error (Issue #40)

Can you please share a sample input file (VCF) and model file (out.model)? This looks like some formatting error in either of those.

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[xwang111]

hi Sethuraman,

I've solved the problem. I replaced the missing sites with reference bases and it worked. But there was another error as below when I performed IMa3 analysis:

command line: ima3_wrapper.py -i test2 -o test2.out -q5 -m0.5 -t1 -b10000 -L10000 --ima-path ~/miniconda3/envs/py-popgen/bin/IMa3

Traceback (most recent call last): File "/home/lilingling/miniconda3/envs/py-popgen/bin/ima3_wrapper.py", line 178, in run(sys.argv[1:]) File "/home/lilingling/miniconda3/envs/py-popgen/bin/ima3_wrapper.py", line 172, in run call_ima3(misc_args,ima_arglist) File "/home/lilingling/miniconda3/envs/py-popgen/bin/ima3_wrapper.py", line 147, in call_ima3 raise Exception("Error with IMa call:%d\n%s"%(ima_call.returncode,ima_stderr)) Exception: Error with IMa call:36 IMa3: data not compatible with infinite sites model - locus #: 0, name: Chr01:797055:798603, sequence#: 47

But I have already done the four-gamete test (using vcf_four_gamete.py), and I'm confused as why it still reports this error.