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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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SAIGE step2 error #360

Closed lanjblue closed 2 years ago

lanjblue commented 3 years ago

I just installed the newest SAIGE version using docker://wzhou88/saige:0.44.6.1. On the second step, it failed with the following error msg:

16805 samples have been used to fit the glmm null model Leave chromosome 7 out will be applied chromosome 1 model results are removed to save memory chromosome 2 model results are removed to save memory chromosome 3 model results are removed to save memory chromosome 4 model results are removed to save memory chromosome 5 model results are removed to save memory chromosome 6 model results are removed to save memory chromosome 8 model results are removed to save memory chromosome 9 model results are removed to save memory chromosome 10 model results are removed to save memory chromosome 11 model results are removed to save memory chromosome 12 model results are removed to save memory chromosome 13 model results are removed to save memory chromosome 14 model results are removed to save memory chromosome 15 model results are removed to save memory chromosome 16 model results are removed to save memory chromosome 17 model results are removed to save memory chromosome 18 model results are removed to save memory chromosome 19 model results are removed to save memory chromosome 20 model results are removed to save memory chromosome 21 model results are removed to save memory chromosome 22 model results are removed to save memory Single variance ratio is provided, so categorical variance ratio won't be used! variance Ratio is 0.9931717 94863 sample IDs are found in sample file isCondition is FALSE Setting genomic region 7:1:250000000 WARNING: Open VCF failed [1] 94863 4 [1] "IID" "IndexInModel" "IndexDose.x" "IndexDose.y" 16805 samples were used in fitting the NULL glmm model and are found in sample file sparse kinship matrix is not used Missing dosages will be mean imputed for the analysis Analysis started at 1627062466 Seconds minMAC: 1 minMAF: 0 Minimum MAF of markers to be tested is 2.975305e-05 It is a binary trait Analyzing 290 cases and 16515 controls isCondition is FALSE Analysis started at 1627062466 Seconds Warning: missing FMT field (DS) Error in if (markerInfo >= 0 & markerInfo <= 1) { : argument is of length zero Calls: SPAGMMATtest Execution halted

I don't understand what's wrong?

thank you!

michelemarongiu79 commented 2 years ago

Hi lanjblue, i have the same error. Were you able to solve?

lanjblue commented 2 years ago

For that analysis, I wasn't able to fix the problem, so I switched back to older version 0.42.1.

weizhouUMICH commented 2 years ago

Sorry for the very late reply! We have just released a new version 1.0.0. It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/ The program will be maintained by multiple SAIGE developers there. The docker image has been updated. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei