...错及解决过程：
gatk报错 An index is required but was not found for file drivingVariantFile
这个报错是因为GATK读别的软件生成的vcf.gz文件，需要一个索引
所以使用bcftools建立索引
bcftools index -t filter1.vcf.gz#-t 建立tbi索引
但此时bcftools又报...
使用linx shell编程时遇到进制问题的报错“value too great for base”：
for a in {001..009}; do
b=$(printf "%03d" $(($a+1)))
if [[ -f "./$a.cds" ]] && [[ -f "./$b.cds" ]]; then
echo "python3 -m jcvi.compara.catalog ortholog NH$a NH$b --cscore=.99 --no_strip_names"
fi
done
...
...amanian A, et al."Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles."Proc Natl Acad Sci U S A 2005, 102:15545-15550.
[2] Barbie DA, et al."Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1."Nature 2009, 462:10...
...d an extra protein/gene mapping file (.xml). Notice, the diagrams designed for Mercator4 (X4 ..) are not compatible to Mercator v.3.6 and vice versa.两个注释结果跟pathway的code根本不兼容。
解决：全部换到版本4能用的就解决了，新图效果更好，推荐。
顺便指路...
...pr[[1]]$data[1:5,1:5]
Error in multiExpr[[1]]$data : $ operatoris invalid for atomic vectors
> #2. 查看样本数据是否完整：
> # 检查数据是否正确：
> exprSize = checkSets(multiExpr)
Error in checkSets(multiExpr) :
data does not appear to have the correct format. Conside...
...
.default = col_double(),
ID_REF = col_integer()
)
See spec(...) for full column specifications.
File stored at:
E:/MSC,ossu-9.1/GPL6244.annot.gz
Warning: 1 parsing failure.
row # A tibble: 1 x 5 col row col expected actual file expected <int...
...ection by racon with tgs reads.
- TGS reads type is ont . MINIMAP2_PARAM is -x ava-ont MIN_IDY is 0.3 . MIN_MATCH is 2000 .
INFO : Checking basic args & env end.
INFO : Step 1 , run TGSSeqSplit to split scaffolds into scaftigs(contigs).
INFO...