Preparing annotation files错误

[cvn001]

您好，

我尝试使用PGA构建个性化蛋白库，在试运行PGA包，进行注释分析构建时出错，无法进行后续的分析。 一、使用PrepareAnnotationRefseq2（参考customProDB包的说明），运行命令和错误如下： `> library(customProDB)

library(PGA) transcript_ids <- c("NM_001126112", "NM_033360", "NR_073499", "NM_004448",

• "NM_000179", "NR_029605", "NM_004333", "NM_001127511") pepfasta <- system.file("extdata", "refseq_pro_seq.fasta",
• package="customProDB") CDSfasta <- system.file("extdata", "refseq_coding_seq.fasta",
• package="customProDB") annotation_path <- tempdir() PrepareAnnotationRefseq2(genome='hg19', CDSfasta, pepfasta, annotation_path,dbsnp = NULL, transcript_ids=transcript_ids,splice_matrix=FALSE, ClinVar=FALSE) Build TranscriptDB object (txdb.sqlite) ... Download the refGene table ... OK Download the hgFixed.refLink table ... OK Extract the 'transcripts' data frame ... OK Extract the 'splicings' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK done Prepare gene/transcript/protein id mapping information (ids.RData) ... Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 27180 did not have 16 elements In addition: Warning message: closing unused connection 3 ()`

二、使用PrepareAnnotationEnsembl2，运行命令和错误如下： `> ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",

• host="sep2015.archive.ensembl.org", path="/biomart/martservice",
• archive=FALSE)

  annotation_path <- tempdir() transcript_ids <- c("ENST00000234420", "ENST00000269305", "ENST00000445888",

• "ENST00000257430", "ENST00000508376", "ENST00000288602",
• "ENST00000269571", "ENST00000256078", "ENST00000384871")

  PrepareAnnotationEnsembl2(mart=ensembl, annotation_path=annotation_path,splice_matrix=FALSE, dbsnp=NULL,transcript_ids=transcript_ids, COSMIC=FALSE) Prepare gene/transcript/protein id mapping information (ids.RData) ... done Build TranscriptDB object (txdb.sqlite) ... Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped) Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK done Prepare exon annotation information (exon_anno.RData) ... done Prepare protein coding sequence (procodingseq.RData)... done Prepare protein sequence (proseq.RData) ... done Warning messages: 1: In download.file(url, destfile, quiet = TRUE) : InternetOpenUrl failed: '拒绝登录申请 ' 2: In .infer_chrominfo_from_transcripts_and_splicings(transcripts$tx_chrom, : chromosome lengths and circularity flags are not available for this TxDb object`

同样地，customProDB包中的PrepareAnnotationEnsembl和PrepareAnnotationRefseq也报错。

请您帮我看看如何处理？

谢谢~