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Error when running halLiftover #300

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zwymic00 opened this issue Apr 25, 2024 · 2 comments
Open

Error when running halLiftover #300

zwymic00 opened this issue Apr 25, 2024 · 2 comments

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@zwymic00
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Hello,

I have a .hal file that was created with cactus and then used halBranchMutations to identify insertions, deletions and SNPs along the tree.
As output I received bed files. I then wanted to use halLiftover to have the coordinates based on the same target for each genome including the ancestors. I used the bed files received by halBranchMutations and the same .hal file as input.
However, I get the following error: "hal exception caught: Error converting string to int: Start in input bed line 1"
I also tried to delete the header but this did not help either. Also adding the option --bedType did not remove the error. To me everything in the column start looks convertable to integer.
I attach an example of a bed file used as input.
test.txt
I installed cactus v2.8.1 and am using the hal tools through that. The version of halLiftOver is v2.2

Do I need to change the .bed file received as output from halBranchMutations in a certain way or should this theoretically be compatible?

Thanks,
Michaela

@glennhickey
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"hal exception caught: Error converting string to int: Start in input bed line 1"

is being caused by the two header lines. Fix with

grep -v ^# test.txt > test.fix.txt

you will then get this error

hal exception caught: Error converting string to int: Anc39 in input bed line 1

which you can fix with

--bedType 3

@zwymic00
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Thanks a lot for your prompt answer.
This helped, it works now!

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