prepare_break.pl script error

[cell101]

Hi I'm trying to use TIGER scripts for GBS analysis when I follow the scripts

I found following error message

Use of uninitialized value in concatenation (.) or string at ../prepare_break.pl line 122, line 28.

I think it comes from hmm_play.jar in hmm.out.txt_log -n 2.0 option is exist which is not in github deposit file

[life101@localhost test]$ more hmm.out.txt_log -r allele_count.base_call.txt -o hmm.out.txt -t bi -m -z sample_hmm_model -n 2.0 ...

Also I follow the README instruction and when visualize it,

I found following error message

[life101@localhost test]$ R --slave --vanilla --args 24 visual_out_test.pdf rough_COs.breaks.txt rough_COs.refined.breaks.txt corrected.refined.breaks.txt frequencies_for_bmm.txt sample_sliding_window.breaks.txt < ../plot_genotyping.R [1] "24" [1] "visual_out_test.pdf" [1] "rough_COs.breaks.txt" [1] "rough_COs.refined.breaks.txt" [1] "corrected.refined.breaks.txt" [1] "frequencies_for_bmm.txt" [1] "sample_sliding_window.breaks.txt" Error in Summary.factor(c(3L, 2L, 3L, 1L, 3L, 1L, 2L, 3L, 2L, 4L, 1L, : ‘max’ not meaningful for factors Calls: plot -> plot.default -> Summary.factor Execution halted

I think it is also related to somewhat error from hmm_play.jar step or prepare_break.pl step

I hope this report will help the improvement of TIGER script

[Imoteph]

Dear @cell101 ,

thank you for your report. Currently this project is not under maintenance any more, due to time constraints.

Could you provide somehow the data when you were calling the prepare_break script. So when I find time I could simulate the error.

[cell101]

Dear Imoteph

Thank you for your response I just used github deposit data and followed README instruction When I used hmm.out.txt file from github and run prepare_break.pl script, It OK but when I use hmm.out.test.txt file generated from hmm_play.jar, it shows error message

hmm.out.test.txt_log.txt hmm.out.test.txt here's my hmm.out.test.txt file and its log

rough_COs.test.breaks.txt rough_COs.test.txt and this is results rough_COs.test.txt file generated from prepare_break.pl using hmm.out.test.txt

[Imoteph]

thx for the data, I will try it out but most likely next week, as I am currently on the move (sorry I did not find yet any time to have a look into this, I will come back to this) Therefore I will keep this issue open.

[sdemirci]

Hello,

I came across the same error in prepare_break.pl. The error starts on chromosome 4. Then I compared the hmm.out.txt files and confirmed that the genotypes in chromosome 4 in hmm.out.txt in github folder and the hmm.out.txt from below code is different java -jar hmm_play.jar -r allele_count.base_call.txt -o hmm.out.txt -t bi -z sample_hmm_model

You can recreate the error by first running hmm_play.jar and then prepare_break.pl.

I see that the issue is open for some time already. Are there any plans to work on this issue?

[Imoteph]

Hi sdemirci,

well from next week it became tons of weeks. Problem is that I am overwhelm with other stuffs. I can only say that I will have a look into it, but I do not know when. I try my best.