...raversal by intervals was requested but some input files are not indexed.
Please index all input files:
samtools index SRR3274663.new.sorted.bam
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
这是...
...the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
把files.per.chunk设置成很小，依然这样报错。
请问该怎么解决呢？
...or in GDCprepare(query) :
I couldn't find all the files from the query. Pleasecheck if the directory parameter is right or ‘GDCdownload’downloaded the samples.
我尝试了改路径，下载到我指定的文件夹（因为GDCprepare是默认的GDCdata文件夹）但每次都下不到里面...
...gnoring input
Failed to create bus connection: No such file or directory
please set right --idtype you input to analysis, The example ID types below are supported:
[1] "ACCNUM" "ALIAS" "ENTREZID" "ENZYME" "EVIDENCE"
[6] "EVIDENCEALL" "GENENAME" "GO"...
...: ignoring environment value of R_HOME
--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/
--> R beginners ? I suggest your learning R language: https://study.omicsclass.com/index
Registered S3 methods overwritten by 'treeio':
method ...
... harfbuzz fribidi (OSX)If harfbuzz freetype2 fribidi is already installed, check that 'pkg-config' is in yourPATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file. If pkg-configis unavailable you can set INCLUDE_DIR and LIB_DIR manually via:R CMD INSTALL --configure-vars='INCLUDE_DI...