DiscoverySNPCallerPluginV2 error: size of all positions in snpPosition table=0

[Kreingkrai Nonkum]

Hi ,

I am using Tassel Version: 5.2.80 for my GBS  data on alfalfa genome and I have a problem with DiscoverySNPCallerPluginV2 and SNPQualityProfilerPlugin because the SNPQualityProfilerPlugin shows this error

size of all tags in tag table=313
size of all tissues in tissue table=0
size of all tags in mappingApproach table=2
size of all taxa in taxa table=288
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin - deleteOldData is TRUE: Clearing existing snpQuality data
sublist
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287]
size of all positions in snpPosition table=0

ERROR: No SNP entries found in the SNP Position table.
Please run DiscoverySNPCallerPluginV2 to call SNPs before running this plugin.

And when I try to run the DiscoverySNPCallerPluginV2, This plugin is running fine but It seem like there is no SNP position in the database.

Here are the log files I have created from these two plugin for the troubleshooting,

Can anyone could help me with these issue?

Best,

Kreingrkrai Nonkum

[Lynn Carol Johnson]

It is hard to say what is wrong without knowing anything about your data.  The DiscoverySNPCallerPluginV2 method did not add any SNPs to the DB, which is why the SNPQualityProfilerPlugin did not return data.

 I would start by looking at your mnMAF (minor allele frequency) and mnLCov (Minimum locus coverage) parameters.  Experiment with different values for those parameters and see if that gets your table populated.

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[Kreingkrai Nonkum]

Hi Lynn,

Thanks for quick response, lower the mnLCov parameter makes the plugin works for me thanks again for your suggestion.

Best,

Kreingkrai Nonkum

ในวันที่ วันอังคารที่ 5 เมษายน ค.ศ. 2022 เวลา 11 นาฬิกา 18 นาที 38 วินาที UTC-7 Lynn Johnson เขียนว่า: