MAFToGVCFPlugin Error

[socialhang]

Hi, @baoxingsong :

I had this error in MAFToGVCFPlugin:

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - GenomeSequenceBuilder.chromosomeSequence: chromosome not found

what should I do for my MAF format?

[baoxingsong]

This is our pipeline for the MAFToGVCFPlugin https://github.com/baoxingsong/AnchorWave/blob/master/doc/GATK.md . If it does not work for you, could you please share your data and all the commands?

[socialhang]

Thanks for your reply!

This is my command and data.

anchorwave gff2seq -i chr1.1.raw.small.gff -r raw_chr1.1.small.fa -o chr1.1.cds.fa minimap2 -x splice -t 40 -k 12 -a -p 0.4 -N 20 new_chr1.1.small.fa chr1.1.cds.fa > new_chr1.1.sam minimap2 -x splice -t 40 -k 12 -a -p 0.4 -N 20 raw_chr1.1.small.fa chr1.1.cds.fa > raw_chr1.1.sam anchorwave genoAli -t 40 -v -i chr1.1.raw.small.gff -as chr1.1.cds.fa -r raw_chr1.1.small.fa -a new_chr1.1.sam -ar raw_chr1.1.sam -s new_chr1.1.small.fa -n align.anchors -o alignment.maf -f alignment.f.maf run_pipeline.pl -Xmx76G -debug -MAFToGVCFPlugin -referenceFasta raw_chr1.1.small.fa -mafFile alignment.maf -sampleName chr1.1 -gvcfOutput runpip.gvcf -fillGaps false

data.tar.gz

[socialhang]

Hi，@baoxingsong:

I'm sorry to bother you again. Do you have some results about my data?

best wishes!

[baoxingsong]

data.tar.gz I renamed your chromosomes, it worked. I did not write code of the TASSEL part, and have no idea why that happen. I will forward this message to my TASSEL colleagues.

[socialhang]

Thanks！！！