treated as unmapped - splitGAlignmentsByCut

[yurasong]

Hello, Currently I am using ATACseqQC to try quality accessment of my ATAC-seq data, when I apply splitGAlignmentsByCut function for preparation of heat;ap, it gives this warning message continuously.

[W::sam_parse1] mapped mate cannot have zero coordinate: treated as unmapped

It seems that it indicates the inconsistent of mate information. However, during the alignment, by post-alignment filtration, I only remained the reads who was properly and uniquely mapped.

Here is the final status of input bam file for splitGAlignmentsByCut, checked by samtools flagstat.

48281627 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 48281627 + 0 mapped (100.00% : N/A) 48281627 + 0 paired in sequencing 24163804 + 0 read1 24117823 + 0 read2 48281627 + 0 properly paired (100.00% : N/A) 48281627 + 0 with itself and mate mapped 0 + 0 singletons (0.00% : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)

Could you give a piece of advice is possible? Thanks in advance,

[jianhong]

Could you minimize your bam files to repeat the error and share the files with me? I also want the sessionInfo of your running. Thank you.

[yurasong]

Hello!

Here is the sessionInfo of my running,

R_session.txt

The file, I tried to minimize but it does not work well. Do you have any suggestion?

Thanks in advance,