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A GATK RUNTIME ERROR, Invalid alignment found, alignmentStart > alignemntEnd
Hi, I was in the second step of Genome STRiP, to discover SV. It seems that all "partition" jobs worked fine, except one. The error message looks like this:
ERROR 00:12:01,906 FunctionEdge - Contents of /u/flashscratch/h/hjzhou/biploar_del_discovery_out/deletions100k/logs/SVDiscovery-203.out: ... ##### ERROR stack trace java.lang.RuntimeException: Invalid alignment found, alignmentStart (1231809) > alignemntEnd (1231808) HS2000-887_377:1:1112:13543:35396 81 chr12 1231809 70 62I38S = 1230685 -1124 ATCTCTATCTCTATCTCTATCTGTGCCTATTGATATATCTGTATATATCTATCTAAATCTCTATCTCTATCTCTATCTGTGCCTATTGATATATCTGTAT CA@>EFECFEDBEAHHHIIIHEHGHGIIJIIGIIGIGJJCJJIGFCJIJJIJJIIIHDEGHGIEJGHHHEHGIJIHJJIJJIJJJIJHGHHHFDFFFC@C SA:Z:chr12,1231809,-,56S44M,60,1; MC:Z:100M OC:Z:62M38S RG:Z:LP6005646-DNA_B05 NM:i:62 MQ:i:60 AS:i:57 XS:i:25 ...
I am very new to Genome STRiP and GATK. Any clue or advice would be helpful.