Hi, I am new to data analysis and so far I have been able to navigate Galaxy - thanks for making this available!!!
I am trying to sort a filtered BAM file by query name (its paired end data) using Picard and I get the following error:
48 SortSam on data 15: BAM sorted in queryname order 2.1 GB formatbam database? [bam_index_core] the alignment is not sorted (D7ZQJ5M1_744:8:1101:10000:10609): 64920643 > 64920521 in 16-th chr [bam_index_build2] fail to index the BAM file. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch *** glibc detected *** pyt
I have tried to decipher the message but I don't understand the error. The bam files were originally sorted by coordinates so I know it should be possible to sort.