There was a problem running popins2 place-splitalign

[abcyulongwang]

Hi!

Thank you for developing such great software. He was a great help to me.
I ran popins2 with 579 individuals, and when I ran popins2 place-refalign, there were no errors. But I found that after running popins2 place-refalign, some individuals got the new file "locations_unplaced.txt", but some individuals did not get this file. This caused me to run popins2 place-splitalign with the following error:

But when I run with an individual that gets a "locations_unplaced.txt" result file When popins2 place-splitalign, I got an error like this
I can't figure out what is the reason for this, is my server running out of memory?

this is my command
popins2 place-splitalign -r genome.fa -c supercontigs.fa sample

Really looking forward to hearing from you, because a little advice from you will help me a lot!
Best
yulong

[mrb20045]

Hi!

Thank you for developing such great software. He was a great help to me. I ran popins2 with 579 individuals, and when I ran popins2 place-refalign, there were no errors. But I found that after running popins2 place-refalign, some individuals got the new file "locations_unplaced.txt", but some individuals did not get this file. This caused me to run popins2 place-splitalign with the following error:

But when I run with an individual that gets a "locations_unplaced.txt" result file When popins2 place-splitalign, I got an error like this I can't figure out what is the reason for this, is my server running out of memory?

this is my command popins2 place-splitalign -r genome.fa -c supercontigs.fa sample

Really looking forward to hearing from you, because a little advice from you will help me a lot! Best yulong

Hi
I got the same error Did you fix it ? Thanks

[Krannich479]

Hi @abcyulongwang and @mrb20045,

I looked at @abcyulongwang 's command and noticed that this is likely a problem with the way you specify your input data. You mentioned that you process data of 579 individuals but your command's positional argument <SAMPLE ID> is just "sample". The sample's ID must be unique.

Please verify that all your Popins/Popins2 commands comply with the intended folder structure, i.e:
<work_dir>/<SAMPLE ID>/<SAMPLE ID>.bam

You can find a precise description and a graphical example here.