运行VEP的INSTALL.pl脚本时提取BioPerl-1.6.1.tar.gz的问题

时间：2018-10-11 22:41:05

标签： linux perl

我正在尝试在Linux机器上安装77版本的Variant Effect Predictor（VEP），并在运行perl INSTALL.pl时不断遇到错误。解决了缺少perl模块Archive::Extract的错误后，我遇到了此错误：

Hello! This installer is configured to install v77 of the Ensembl API for use by the VEP.
It will not affect any existing installations of the Ensembl API that you may have.

It will also download and install cache files from Ensembl's FTP server.

Checking for installed versions of the Ensembl API...done

Setting up directories

Downloading required files
 - fetching ensembl
** GET https://github.com/Ensembl/ensembl/archive/release/77.zip ==> 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)
** GET https://github.com/Ensembl/ensembl/archive/release/77.zip ==> 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)
Trying to fetch using curl
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   124    0   124    0     0    730      0 --:--:-- --:--:-- --:--:--   729
100 10.7M    0 10.7M    0     0  3535k      0 --:--:--  0:00:03 --:--:-- 4859k
 - unpacking ./Bio/tmp/ensembl.zip
 - moving files
 - fetching ensembl-variation
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   134    0   134    0     0    737      0 --:--:-- --:--:-- --:--:--   740
100 3986k    0 3986k    0     0  4378k      0 --:--:-- --:--:-- --:--:-- 7182k
 - unpacking ./Bio/tmp/ensembl-variation.zip
 - moving files
 - fetching ensembl-funcgen
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   132    0   132    0     0    798      0 --:--:-- --:--:-- --:--:--   800
100 2016k    0 2016k    0     0  3354k      0 --:--:-- --:--:-- --:--:-- 5156k
 - unpacking ./Bio/tmp/ensembl-funcgen.zip
 - moving files
 - fetching BioPerl
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   178  100   178    0     0   2695      0 --:--:-- --:--:-- --:--:--  2738
100  9340  100  9340    0     0  46698      0 --:--:-- --:--:-- --:--:-- 46698
 - unpacking ./Bio/tmp/BioPerl-1.6.1.tar.gz
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Unable to extract '/opt/vep/src/ensembl-vep/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/tmp/BioPerl-1.6.1.tar.gz': Invalid header block at offset unknown at INSTALL.pl line 905.
Error listing contents of archive '/opt/vep/src/ensembl-vep/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/tmp/BioPerl-1.6.1.tar.gz': /bin/tar: This does not look like a tar archive
/bin/tar: Skipping to next header
/bin/tar: Exiting with failure status due to previous errors
 at INSTALL.pl line 905.
Extract failed due to errors at INSTALL.pl line 905.
Can't call method "error" on an undefined value at INSTALL.pl line 905.

INSTALL.pl脚本的第905行是：

900 # unpack a tarball
901 sub unpack_arch {
902   my ($arch_file, $dir) = @_;
903 
904   my $ar = Archive::Extract->new(archive => $arch_file);
905   my $ok = $ar->extract(to => $dir) or die $ae->error;
906   unlink($arch_file);
907 }

我对perl不够熟悉，无法确切地知道出了什么问题，但是我尝试用tar -xvzf自己对BioPerl-1.6.1.tar.gz进行解压缩，但没有成功。我该如何解决这个问题？

1 个答案:

答案 0 :(得分：0)

此存档似乎已损坏：/opt/vep/src/ensembl-vep/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/tmp/BioPerl-1.6.1.tar.gz

/ bin / tar给您一个错误“ / bin / tar：这看起来不像tar存档”

您可以替换此文件还是将其删除并重新启动安装？

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