Closed jychoilab closed 5 years ago
Jae,
The latest version needs the -v switch for the eagle variants output. In your case, the command should be:
eagle-rc -a data_align2_A.bam --listonly -o Ref_A.sample -v Ref_A.sample.txt Ref_A.sample.readinfo.txt > Ref_A.sample.list
The error is due to the program trying to parse Ref_A.sample.txt as the readinfo.txt
Hi Tony
Sorry I should have said that I tried the -v switch and got the error message. Without the -v switch I get the error message:
Missing EAGLE output file!
Jae
Hi Jae,
Thanks for the data. The issue was the flag field was empty as that is valid when using single-end reads. I've solved the issue and updated the code.
I also suggest you try the --ngi mode to perhaps simplify your workflow, though it doesn't have the advantage of using explicit genotype information as in the default workflow.
Hi Tony
Thanks with the fix I don't have the issue anymore. But I'll try the --ngi mode since it seems like it'll be something that's more suitable for my case.
Jae
Dear, Tony
I've been playing around with the eagle pipeline also following the example script for an allopolyploid case I have. Its not exactly an allopolyploid, but I have an F1 hybrid transcriptome data set and have both parents reference genome. I got upto the step
eagle-rc -a data_align2_A.bam --listonly -o Ref_A.sample Ref_A.sample.txt Ref_A.sample.readinfo.txt > Ref_A.sample.list
But get the following error
ERROR: (eagle-rc.c:149: errno: None) bad fields in EAGLE read info file
I can send some of the files I've generated to get to the step if you want as well.
Sincerely,
Jae