I want to use "Adding to a node" to adding the new genome of chicken to the 363-avian-2020.hal. So I used the add_to_node.txt ( (chickenGRCg7b, Gallus_gallus:0.0441471,Coturnix_japonica:0.0656888)birdAnc333; ) file and got the "add_to_node.hal " file successfully.
However, when I use the following commnads "halReplaceGenome --bottomAlignmentFile add_to_node.hal --topAlignmentFile 363-avian-2020.hal 363-avian-2020.hal birdAnc333 ", it reports "what(): Cannot update sequence birdAnc333refChr4210 because it is not present in genome birdAnc333".
I have checked the file add_to_node.hal and 363-avian-2020.hal and used hal2fasta to extract the genome of birdAc333.
add_to_node.hal does not have sequence birdAnc333refChr4210 but 363-avian-2020.hal do have.
I also extract the aligment of birdAnc333refChr4210 from 363-avian-2020.hal. It shows a small sequence as follows:
a
s birdAnc333.birdAnc333refChr4230 0 8 + 8 AGAGAACA
s Gallus_gallus.chr13 2368436 8 + 17760035 AGAGAACA
is there any way to solve this problem? or is there any way I can remove the aligment of birdAnc333refChr4230 because it seems does not matter.
I want to use "Adding to a node" to adding the new genome of chicken to the 363-avian-2020.hal. So I used the add_to_node.txt ( (chickenGRCg7b, Gallus_gallus:0.0441471,Coturnix_japonica:0.0656888)birdAnc333; ) file and got the "add_to_node.hal " file successfully. However, when I use the following commnads "halReplaceGenome --bottomAlignmentFile add_to_node.hal --topAlignmentFile 363-avian-2020.hal 363-avian-2020.hal birdAnc333 ", it reports "what(): Cannot update sequence birdAnc333refChr4210 because it is not present in genome birdAnc333". I have checked the file add_to_node.hal and 363-avian-2020.hal and used hal2fasta to extract the genome of birdAc333.
add_to_node.hal does not have sequence birdAnc333refChr4210 but 363-avian-2020.hal do have. I also extract the aligment of birdAnc333refChr4210 from 363-avian-2020.hal. It shows a small sequence as follows: a s birdAnc333.birdAnc333refChr4230 0 8 + 8 AGAGAACA s Gallus_gallus.chr13 2368436 8 + 17760035 AGAGAACA
is there any way to solve this problem? or is there any way I can remove the aligment of birdAnc333refChr4230 because it seems does not matter.