GAF file empty with vg giraffe about vg

[xchang1]

@jltsiren I think this is a problem with the minimizers. There were a bunch of errors like this
MinimizerIndex::find_offset(): Cannot find the offset for key 66075703255364729

[jltsiren]

It sounds like the minimizer index is corrupted. You could try rebuilding it with:

vg minimizer -p -d graph.dist -o graph.min graph.gbz

Also, are what does the vg giraffe command output during initialization? Are there any errors/warnings?

[m-bogaerts]

Hello again,

It worked perfectly after rebuilding the minimizer index! Now I am getting this GAF output:

D00562:114:C94WFANXX:7:1111:1229:2161	125	0	125	+	<48413770<48413771<48413772<48413773<48413775<48413776<48413778<48413779<48413780<48413781<48413782	173	7	131	124	125	60	AS:i:130	bq:Z:CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	cs:Z::76*AG:48	dv:f:0.008	fn:Z:D00562:114:C94WFANXX:7:1111:1229:2161	pd:b:1

I used to get these outputs while running vg giraffe (which I haven't gotten right now):

MinimizerIndex::find_offset(): Cannot find the offset for key 237432784254556
MinimizerIndex::find_offset(): Cannot find the offset for key 3709887253977
MinimizerIndex::find_offset(): Cannot find the offset for key 229929871826950668
MinimizerIndex::find_offset(): Cannot find the offset for key 68746704681186812
T19:    All minimizers:
T19:    00000000000000000000000000000000000000000000000000000000000000000000000000000000
000000000000000000001111111111111111111111111
T19:    00000000001111111111222222222233333333334444444444555555555566666666667777777777
888888888899999999990000000000111111111122222
T19:    01234567890123456789012345678901234567890123456789012345678901234567890123456789
012345678901234567890123456789012345678901234
T19:    CGATTCGATGGGGTTTGAAAGACATCACTTCACTGCTACCTGTTTTTAACCNTGATGACCAACTTATAGGCGAGATTATT
CCGTAAAGGATTTTTTTTCATTATAATTGAATATTTAGCTGCAAT
T19:    -------ATGGGGTTTGAAAGACATCACTTCACTGC---------- (#0, 0 hits)
T19:            --------AAACAGGTAGCAGTGAAGTGATGTCTTTC---------- (#2, 0 hits)
T19:                     ---TTAAAAACAGGTAGCAGTGAAGTGATGTC---------- (#3, 0 hits)

Thank you very much!!