If you run minibwa with non-existent input data, the program prints out suitable error messages. However, it produces a return code of 0. This means an automated workflow may miss the failure and happily continue executing producing junk. (As an aside, if the index doesn't exist a suitable error code is returned).
scott@n12$ minibwa map t2t/chm13v2.0.fa f1 f2
[M::main_map::24.317*0.12] index loaded
@HD VN:1.6 SO:unsorted GO:query
@SQ SN:chr1 LN:248387328
...
@SQ SN:chrM LN:16569
@PG ID:minibwa PN:minibwa VN:0.7-r421 CL:minibwa map t2t/chm13v2.0.fa f1 f2
ERROR: failed to open file 'f1': No such file or directory
[M::main] Version: 0.7-r421
[M::main] CMD: minibwa map t2t/chm13v2.0.fa f1 f2
[M::main] Real time: 24.329 sec; CPU: 2.935 sec; Peak RSS: 6.719 GB
[scott@n12$ echo $?
0
Version: 0.7-r421
If you run
minibwawith non-existent input data, the program prints out suitable error messages. However, it produces a return code of 0. This means an automated workflow may miss the failure and happily continue executing producing junk. (As an aside, if the index doesn't exist a suitable error code is returned).Version: 0.7-r421