Mismatched UMI of a pair of reads

[litun-fkby]

hello, I meet some mistake with the gencore (Version: 0.17.2):
1 contigs in the bam file:
chr1: 7249 bp

Mismatched UMI of a pair of reads
Left:
0:0, M:0:0 TLEN:0 ID:0
E100030802L1C001R00101395324:umi_CA_NN
TTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTATTATTAATATTATTATTAATTTTAAAATCACAACAAAATACAAAAAACAAAAAAAAAAA
GGGGGHHGGHIGGGGGHGGGIIGGGGGGGGGGIGGGGHGIHGGGGGGHGGGGGGGGIGGGGGGHGGGHIGIGGGGGIIGGHHGGGGHIGGHG
Right:
0:0, M:0:0 TLEN:0 ID:0
E100030802L1C004R03200085905:umi_CG_NN
TTAAAAAATTATAAAAAAAAAATAAAAAAATAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
ERROR: The UMI of a read pair should be identical, but we got CA_ and CG_

but, when i find the reads in original bam ,the reads pair seem to be correct with same UMI :

it's seem like the gencore consider the two read with different read name to be one pair read.

the command is:
gencore --umi_prefix=umi -s 3 --ref hg19.fasta --quit_after_contig 25 -i input.bam -o output.umi.bam

but when I add the "-d" parameter,there is no mistake , maybe there has some difference,:
gencore --umi_prefix=umi -d 0 -s 3 --ref hg19.fasta --quit_after_contig 25 -i input.bam -o output.umi.bam

Looking forward to your reply!

[baoyl818]

I have met the same problem, looking forward other response.

Besides, I have tried the following method to solve it:
before running the genecore , add this cmd:
samtools view -@ $threads -bh -f 2 in.bam > out.bam
to remove the unpair reads, and it works ok.