Piranha peak calling waring message?

Question

[PK]

Hi,

I'm doing peak calling with piranha. But I'm getting a warning message by saying

WARNING: Skipped 1376269 in BAM file sorted_SRR3290136_v6.bam due to unknown reference IDs

My input bam file sorted look like this

BAM_ID.481964   272 1   15116   1   39M *   0   0        
BAM_ID.902082   272 1   15116   1   39M *   0   0    
BAM_ID.1031822  272 1   15116   1   39M *   0   0    
BAM_ID.1504529  272 1   15116   1   39M *   0   0    
BAM_ID.1547816  272 1   15116   1   39M *   0   0    
BAM_ID.1876598  272 1   15116   1   39M *   0   0   

The bam files mapped by STAR and sorted by co-ordinates

[Pierre Lindenbaum]

is it this sofware ? https://github.com/smithlabcode/piranha

this tools takes a BED as input, not a bam/sam as above. Otherwise, show us your full command line...

[PK]

Sure i Guess it takes three possible inputs , bed, bam and xml file. And i tried both bam and bed file it shows same waring message

 Piranha sorted _v6.bam -b 50 -o  v6_v1.bed 

 WARNING: Skipped 6366550 in BAM file