warning messages in generating the annotated GDS (aGDS) file.

[jingydz]

used (Mb) gc trigger (Mb) max used (Mb) Ncells 283209 15.2 664320 35.5 450929 24.1 Vcells 487102 3.8 8388608 64.0 1815714 13.9 [1] 624684 22 Warning messages: 1: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 2: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 3: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 4: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 5: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 6: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 7: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 8: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 9: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "".

load("/xxx/rare_variant/association/pre_step/jobs_num.Rdata") ls() [1] "jobs_num" jobs_num

1. chr start_loc end_loc individual_analysis_num sliding_window_num scang_num
2. 1 1 NA NA NA NA NA
3. 2 2 NA NA NA NA NA
4. 3 3 NA NA NA NA NA
5. 4 4 NA NA NA NA NA
6. 5 5 NA NA NA NA NA
7. 6 6 NA NA NA NA NA
8. 7 7 NA NA NA NA NA
9. 8 8 NA NA NA NA NA
10. 9 9 NA NA NA NA NA
11. 10 10 NA NA NA NA NA
12. 11 11 NA NA NA NA NA
13. 12 12 NA NA NA NA NA
14. 13 13 NA NA NA NA NA
15. 14 14 NA NA NA NA NA
16. 15 15 NA NA NA NA NA
17. 16 16 NA NA NA NA NA
18. 17 17 NA NA NA NA NA
19. 18 18 NA NA NA NA NA
20. 19 19 NA NA NA NA NA
21. 20 20 NA NA NA NA NA
22. 21 21 NA NA NA NA NA
23. 22 22 NA NA NA NA NA

[xihaoli]

Hi @jingydz,

These warning messages indicate that some of the missing characters in the annotation database will be converted to an empty string "" when integrating into the aGDS file, so they are not errors.

It seems like your jobs_num object is empty, which is unexpected. What did you use in your Association_Analysis_PreStep.r?

Best, Xihao