Closed wangshuang2024 closed 7 months ago
Hi @wangshuang2024,
Thanks for reaching out. The gds_file_name_1
and gds_file_name_2
are both part of the target gds file name, separated by the chr
number. For example, if the target gds file is for chromosome 1, and
gds_file_name_1 <- "freeze.5.chr"
gds_file_name_2 <- ".pass_and_fail.gtonly.minDP0.gds"
then after string concatenation, the target GDS file should have name freeze.5.chr1.pass_and_fail.gtonly.minDP0.gds
.
Hope this helps.
Best, Xihao
Hi @wangshuang2024,
Thanks for reaching out. The
gds_file_name_1
andgds_file_name_2
are both part of the target gds file name, separated by thechr
number. For example, if the target gds file is for chromosome 1, andgds_file_name_1 <- "freeze.5.chr" gds_file_name_2 <- ".pass_and_fail.gtonly.minDP0.gds"
then after string concatenation, the target GDS file should have name
freeze.5.chr1.pass_and_fail.gtonly.minDP0.gds
.Hope this helps.
Best, Xihao
Thank you , I got it.
Hello, @xihaoli . I got another problem and hope you can help me. In step 2 Annotate the variants. for i in 'seq 1 22'; do Rscript /Rscript/staarpipeline/Annotate.R ${i}; done After I run this code. I got an error.
Warning message: NAs introduced by coercion Error in 1:chr_splitnum : NA/NaN argument Execution halted
How can I solve this? Thank you for your help.
Hi @wangshuang2024,
It seems like your chr_splitnum
in line 33 of Annotate.R is NA
. Can you make sure whether the path of your file_DBsplit
is set correctly? You may perform a manual check by setting chr <- 1
in line 24 of Annotate.R).
Thanks, Xihao
Hi @wangshuang2024,
It seems like your
chr_splitnum
in line 33 of Annotate.R isNA
. Can you make sure whether the path of yourfile_DBsplit
is set correctly? You may perform a manual check by settingchr <- 1
in line 24 of Annotate.R).Thanks, Xihao
Thank you, @xihaoli . I figure out this problem. There is another error.
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 269061 14.4 654582 35 444042 23.8 Vcells 448538 3.5 8388608 64 1771786 13.6 [1] 1 No such file or directory (os error 2) [1] 2 No such file or directory (os error 2) [1] 3 No such file or directory (os error 2) Selector index 1 is out of bounds. Index must be >= 1 and <= 0.
I check the path of "file_DBsplit","DB_path“,”xsv” and "output_path", they are all correct.
DB name like this "/reference/FAVOR/essentialDB/chr1.tar.gz"
Hi @wangshuang2024,
You would need to first uncompress the chr1.tar.gz
file before running Annotate.R.
Best, Xihao
Hi @wangshuang2024,
You would need to first uncompress the
chr1.tar.gz
file before running Annotate.R.Best, Xihao
Thank you, Xihao. I solve these problems.
Hello, @xihaoli. In the script of "Varinfo_gds.R" and "gds2agds.R", it has two gds name.
gds_file_name_1 <- "freeze.5.chr" gds_file_name_2 <- ".pass_and_fail.gtonly.minDP0.gds"
I wonder what the two documents represent and how they are produced? Thank you.