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tony-kuo / eagle

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ERROR: (eagle-rc.c:149: errno: None) bad fields in EAGLE read info file #1

Closed jychoilab closed 5 years ago

jychoilab commented 5 years ago

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

ghost commented 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

jychoilab commented 5 years ago

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

ghost commented 5 years ago

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.

jychoilab commented 5 years ago

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