Comments (7)
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
from staarpipeline-tutorial.
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.
from staarpipeline-tutorial.
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.
from staarpipeline-tutorial.
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
from staarpipeline-tutorial.
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_pathโ๏ผโxsvโ and "output_path", they are all correct.
DB name like this "/reference/FAVOR/essentialDB/chr1.tar.gz"
from staarpipeline-tutorial.
Hi @wangshuang2024,
You would need to first uncompress the chr1.tar.gz
file before running Annotate.R.
Best,
Xihao
from staarpipeline-tutorial.
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.
from staarpipeline-tutorial.
Related Issues (20)
- fit_nullmodel Output is mostly Null and 0 HOT 16
- Fitting NULL model for binary outcomes HOT 5
- Error in Gene Centric Analysis HOT 1
- Error in results_plof_genome[, "cMAC"] : subscript out of bounds HOT 2
- Followup Question to Issue #28 HOT 2
- STAARpipeline_Gene_Centric_Noncoding HOT 2
- Dynamic Window dim(X) error HOT 3
- Can't annotate individual variant results HOT 2
- [Suggestion-Implementation] Add information to summary and annotations of results HOT 1
- Conditional analysis - Summary Gene Centric Noncoding not running to completion HOT 6
- Ukbiobank Agds files generation HOT 16
- Plots for gene centric ncRNA regions HOT 5
- FATAL ERROR - Too many first alleles as the major allele (~21.5%). HOT 1
- warning messages in generating the annotated GDS (aGDS) file. HOT 3
- Controls / cases counts inverted when using binary model HOT 7
- kinship matrix HOT 2
- variant set in gene-centric coding/noncoding analysis HOT 2
- in the Step 2: Individual (single-variant) analysis, Error in if (chr == 1) { : argument is of length zero HOT 3
- Error : Mat::operator(): index out of bounds & Error in apply(emthr_SCANG_O, 2, max) : HOT 1
- What is the difference between the "results_temp" and "results_m" results? HOT 1
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