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ctlab / GADMA

Genetic Algorithm for Demographic Model Analysis
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example Error #2

Closed Sh1ne111 closed 5 years ago

Sh1ne111 commented 5 years ago

hi, when i run gadma ,i got a error "$ gadma -i data.txt -o gadma_out

Warning: Theta0 is not specified. It would be 1.0.

Warning: Time for one generation is not specified. Time will be in genetic units.

Traceback (most recent call last): File "/public1/home/Sh1ne/anaconda2/bin/gadma", line 11, in load_entry_point('gadma==1.0.0', 'console_scripts', 'gadma')() File "/public1/home/Sh1ne/anaconda2/lib/python2.7/site-packages/gadma-1.0.0-py2.7.egg/gadma/core.py", line 150, in main params = options.parse_args() File "/public1/home/Sh1ne/anaconda2/lib/python2.7/site-packages/gadma-1.0.0-py2.7.egg/gadma/options.py", line 911, in parse_args options_storage.check() File "/public1/home/Sh1ne/anaconda2/lib/python2.7/site-packages/gadma-1.0.0-py2.7.egg/gadma/options.py", line 509, in check self.input_file, self.ns, self.pop_labels) File "/public1/home/Sh1ne/anaconda2/lib/python2.7/site-packages/gadma-1.0.0-py2.7.egg/gadma/support.py", line 250, in load_spectrum return READ_ALLOWED_EXTENSIONS[ext](filename, proj, pop_labels) File "/public1/home/Sh1ne/anaconda2/lib/python2.7/site-packages/gadma-1.0.0-py2.7.egg/gadma/support.py", line 219, in read_dadi_file for x in xrange(number_of_pops) ValueError: invalid literal for int() with base 10: 'ASW'"

how to sovle this problem?

noscode commented 5 years ago

Hi, ChenSh1ne,

It seems like a wrong txt file. The error occurs because the columns with number of chromosomes with SNP in each population are taken as int values in order to calculate the total number of chromosomes. The error seems to happen in the first or the second line of txt file.

Could you please send the first two lines or check by yourself that:

For example this is valid txt file (two first lines): gillettii intermedia Allele1 CO WY Allele2 CO WY Contig Position -G- --- G 7 16 A 3 0 comp20839_c0_seq1 1704

I think that there is some additional commented string or something else, as 'ASW' looks like label for population from the first string.

Best wishes, Ekaterina Noskova

Sh1ne111 commented 5 years ago

Hi，Ekaterina Noskova, Sorry to reply so late, I use a dadi example data as a gadma input, its format like this:

This data is a subset of the EGP data used in the original dadi paper.

Human Chimp Allele1 ASW YRI CEU MXL CHB JPT Allele2 ASW YRI CEU MXL CHB JPT Gene Position TTA TTA T 27 22 43 42 23 22 G 3 2 1 2 1 2 abcb1 77 GCT GCT C 27 22 43 42 23 22 T 3 2 1 2 1 2 abcb1 145 ACG ATG C 29 24 44 44 24 24 T 1 0 0 0 0 0 abcb1 289 GCG GCG C 30 24 44 43 24 24 T 0 0 0 1 0 0 abcb1 367 ACG ACG C 30 24 43 44 24 24 T 0 0 1 0 0 0 abcb1 391

Could you please help me check what the problem is?

noscode commented 5 years ago

Dear ChenSh1ne,

It did not work because of the first commented line: # This data is a subset of the EGP data used in the original dadi paper.

I have fixed this bug in new commit and now this file is properly readable. Thank you for your issue.

However please pay attention that GADMA can hold up to three populations, but this file contains information for 6. So you would probably want to specify parameters file.

Best, Ekaterina

Sh1ne111 commented 5 years ago 
        got it!  It works,thanks u very much!☺️

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        On 08/12/2019 18:17, Ekaterina Noskova wrote: Dear  ChenSh1ne,

It did not work because of the first commented line:

This data is a subset of the EGP data used in the original dadi paper.

I have fixed this bug in new commit and now this file is properly readable. Thank you for your issue. However please pay attention that GADMA can hold up to three populations, but this file contains information for 6. So you would probably want to specify parameters file. Best, Ekaterina

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noscode commented 5 years ago

You are welcome!