I'm running a Perl script from the EMBL (found here https://github.com/EMBL-EBI-GCA/reseqtrack/blob/master/scripts/variation_data/calculate_allele_frq_from_vcf.pl) Under Ubuntu 16.10 I have installed Vcftools and Tabix as is required and both have been tested to work accordingly. I execute the script with the following command:
perl /home/[user]/calculate_allele_frq_from_vcf.pl \
-vcf /home/[user]/share/1000genomesPhase3VCFFiles/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \
-sample_panel /home/[user]/share/1000genomesPhase3VCFFiles/integrated_call_samples_v3.20130502.ALL.panel \
-out_dir /home/[user]/Desktop/AlleleFrequency \
-tabix /home/[user]/tabix-0.2.6 \
-vcftools_dir /home/[user]/vcftools_0.1.13 \
-region 1:1-10000 \
-pop CEU,FIN \
This returns the following error
Smartmatch is experimental at /home/[user]/calculate_allele_frq_from_vcf.pl line 133.
Smartmatch is experimental at /home/[user]/calculate_allele_frq_from_vcf.pl line 144.
sh: 1: /home/[user]/tabix-0.2.6: Permission denied
Broken VCF header, no column names?
at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
Vcf::throw(Vcf4_2=HASH(0x55761601d320), "Broken VCF header, no column names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 866
VcfReader::_read_column_names(Vcf4_2=HASH(0x55761601d320)) called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
VcfReader::parse_header(Vcf4_2=HASH(0x55761601d320)) called at /home/[user]/vcftools_0.1.13/perl/vcf-subset line 121
main::vcf_subset(HASH(0x557615b24558)) called at /home/[user]/vcftools_0.1.13/perl/vcf-subset line 12
Broken VCF header, no column names?
at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
Vcf::throw(Vcf4_2=HASH(0x55fa53436f60), "Broken VCF header, no column names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 866
VcfReader::_read_column_names(Vcf4_2=HASH(0x55fa53436f60)) called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
VcfReader::parse_header(Vcf4_2=HASH(0x55fa53436f60)) called at /home/[user]/vcftools_0.1.13/perl/fill-an-ac line 45
main::fill_an_ac(undef) called at /home/[user]/vcftools_0.1.13/perl/fill-an-ac line 9
sh: 1: /home/[user]/tabix-0.2.6: Permission denied
Broken VCF header, no column names?
at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
Vcf::throw(Vcf4_2=HASH(0x5607d059a190), "Broken VCF header, no column names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 866
VcfReader::_read_column_names(Vcf4_2=HASH(0x5607d059a190)) called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
VcfReader::parse_header(Vcf4_2=HASH(0x5607d059a190)) called at /home/[user]/vcftools_0.1.13/perl/vcf-subset line 121
main::vcf_subset(HASH(0x5607d00a1558)) called at /home/[user]/vcftools_0.1.13/perl/vcf-subset line 12
Broken VCF header, no column names?
at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 172.
Vcf::throw(Vcf4_2=HASH(0x556b8e952110), "Broken VCF header, no column names?") called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 866
VcfReader::_read_column_names(Vcf4_2=HASH(0x556b8e952110)) called at /home/[user]/vcftools_0.1.13/perl/Vcf.pm line 601
VcfReader::parse_header(Vcf4_2=HASH(0x556b8e952110)) called at /home/[user]/vcftools_0.1.13/perl/fill-an-ac line 45
main::fill_an_ac(undef) called at /home/[user]/vcftools_0.1.13/perl/fill-an-ac line 9
/home/[user]/Desktop/AlleleFrequency/calculated_fra.process3085.1.1-10000.CEU_FIN
It appears that the script doesn't have permission to access Tabix for some reason. I've given the folder full read/write permission for the user executing the script (me). Any ideas?
You set -tabix to /home/[user]/tabix-0.2.6, but the code seems to need the path to the executable, not the top directory. Adding /bin/tabix to the path should probably fix the problem.
I am trying to install lumen with composer so I used the command below
composer create-project --prefer-dist laravel/lumen api
But, for some reason I am getting this error before even doing anything, just visiting the public folder.
Sorry, the page you are looking for could not be found.
1/1
NotFoundHttpException in RoutesRequests.php line 442:
in RoutesRequests.php line 442
at Application->handleDispatcherResponse(array('0')) in RoutesRequests.php line 381
at Application->Laravel\Lumen\Concerns{closure}() in RoutesRequests.php line 624
at Application->sendThroughPipeline(array(), object(Closure)) in RoutesRequests.php line 382
at Application->dispatch(null) in RoutesRequests.php line 327
at Application->run() in index.php line 28
Assuming you are running lumen from a subdirectory, in public/index.php change:
$app->run();
to
$request = Illuminate\Http\Request::capture();
$app->run($request);
That did the trick for me.
I cannot for the life of me figure out how to setup Bugzilla to send email using TLS. I got the Bugzilla site running, however, when I try to change my Bugzilla account email, the system fails with the following (I setup my email parameters to use my Amazon AWS email server):
An unexpected error occurred. This could be a temporary problem, or some code is behaving incorrectly. If this problem persists, please email this page to ...#.....com with details of what you were doing at the time this message appeared.
URL: http://example.com/userprefs.cgi?new_password1=&new_password2=&tab=account&old_login=jdoe%40example.com&realname=John%20Doe&new_login_name=johndoe422%40example.net&dosave=1&token=...&old_password=...
There was an error sending mail from 'bugzilla#example.com' to 'johndoe422#example.com': failed AUTH: Must issue a STARTTLS command first
Traceback:
at Bugzilla/Mailer.pm line 186.
Bugzilla::Mailer::MessageToMTA(...) called at Bugzilla/Token.pm line 116
Bugzilla::Token::IssueEmailChangeToken(...) called at /srv/www/bugzilla/userprefs.cgi line 120
main::SaveAccount(...) called at /srv/www/bugzilla/userprefs.cgi line 608
So I proceeded to try to fix this problem by following the instructions in: Bugzilla Alerts Using Gmail
I managed to install the Email::Send::SMTP::TLS module using cpanm (Not sure why I just cannot install any module via CPAN at all), after installation, the SMTP::TLS option does not appear in the drop-down. I just ignored it and continue to update Mailer.pm as instructed.
After that, when I refresh my bugzilla page, I get the following error:
Software error:
Global symbol "#args" requires explicit package name at Bugzilla/Mailer.pm line 138.
Global symbol "#args" requires explicit package name at Bugzilla/Mailer.pm line 144.
Compilation failed in require at Bugzilla/Auth.pm line 22.
BEGIN failed--compilation aborted at Bugzilla/Auth.pm line 22.
Compilation failed in require at Bugzilla.pm line 23.
BEGIN failed--compilation aborted at Bugzilla.pm line 23.
Compilation failed in require at /srv/www/bugzilla/editparams.cgi line 15.
BEGIN failed--compilation aborted at /srv/www/bugzilla/editparams.cgi line 15.
For help, please send mail to this site's webmaster, giving this error message and the time and date of the error.
I've read that perhaps it is because Email::Send::SMTP::TLS requires Net::SSLeay package. So I proceed to try to install it using cpanm. However, cpanm fails with the following log:
23 *** Found OpenSSL-1.0.1f installed in /usr
24 *** Be sure to use the same compiler and options to compile your OpenSSL, perl,
25 and Net::SSLeay. Mixing and matching compilers is not supported.
26 Do you want to run external tests?
27 These tests *will* *fail* if you do not have network connectivity. [n] n
28 Checking if your kit is complete...
29 Looks good
30 Generating a Unix-style Makefile
31 Writing Makefile for Net::SSLeay
32 Writing MYMETA.yml and MYMETA.json
33 -> OK
34 Checking dependencies from MYMETA.json ...
35 Checking if you have Test::More 0.60_01 ... Yes (1.001014)
36 Checking if you have MIME::Base64 0 ... Yes (3.13)
37 Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.10)
38 Building and testing Net-SSLeay-1.72
39 cp lib/Net/SSLeay.pm blib/lib/Net/SSLeay.pm
40 AutoSplitting blib/lib/Net/SSLeay.pm (blib/lib/auto/Net/SSLeay)
41 blib/lib/Net/SSLeay.pm: some names are not unique when truncated to 8 characters:
42 directory blib/lib/auto/Net/SSLeay:
43 do_https3.al, do_https2.al, do_https4.al, do_https.al truncate to do_https
44 do_httpx3.al, do_httpx2.al, do_httpx4.al truncate to do_httpx
45 get_https.al, get_https3.al, get_https4.al, get_http.al, get_http3.al, get_http4.al, get_httpx.al, get_httpx3.al, get_httpx4.al truncate to get_http
46 head_https.al, head_https3.al, head_https4.al, head_http.al, head_http3.al, head_http4.al, head_httpx.al, head_httpx3.al, head_httpx4.al truncate to head_htt
47 post_https.al, post_https3.al, post_https4.al, post_http.al, post_http3.al, post_http4.al, post_httpx.al, post_httpx3.al, post_httpx4.al truncate to post_htt
48 put_https.al, put_https3.al, put_https4.al, put_http.al, put_http3.al, put_http4.al, put_httpx.al, put_httpx3.al, put_httpx4.al truncate to put_http
49 ssl_read_all.al, ssl_read_until.al, ssl_read_CRLF.al truncate to ssl_read
50 ssl_write_all.al, ssl_write_CRLF.al truncate to ssl_writ
51 tcp_read_all.al, tcp_read_until.al, tcp_read_CRLF.al truncate to tcp_read
52 tcp_write_all.al, tcp_write_CRLF.al truncate to tcp_writ
53 cp lib/Net/SSLeay/Handle.pm blib/lib/Net/SSLeay/Handle.pm
54 cp lib/Net/SSLeay.pod blib/lib/Net/SSLeay.pod
55 Running Mkbootstrap for Net::SSLeay ()
56 chmod 644 "SSLeay.bs"
57 "/usr/bin/perl" "-Iinc" "/usr/share/perl/5.18/ExtUtils/xsubpp" -typemap "/usr/share/perl/5.18/ExtUtils/typemap" -typemap "typemap" SSLeay.xs > SSLeay.xsc && mv SSLeay.xsc SSL eay.c
58 cc -c -I/usr/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.72\" -DXS_VERSION=\"1.72\" -fPIC "-I/usr/lib/perl/5.18/CORE" SSLeay.c
59 {standard input}: Assembler messages:
60 {standard input}: Error: open CFI at the end of file; missing .cfi_endproc directive
61 cc: internal compiler error: Killed (program cc1)
62 Please submit a full bug report,
63 with preprocessed source if appropriate.
64 See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
65 make: *** [SSLeay.o] Error 4
66 -> FAIL Installing Net::SSLeay failed. See /home/ubuntu/.cpanm/work/1443609644.32449/build.log for details. Retry with --force to force install it.
I do not know perl and cannot figure out why I'm getting errors left and right.
I read in many places that I can simply install all available packages using command like:
/usr/bin/perl install-module.pl --all
However, this command does not work for me. (I can't install any modules using CPAN at all, not sure why) It pretty much just does nothing for me. This is the output I get when execute install-module.pl:
ubuntu#ip-10-130-10-107:/srv/www/bugzilla$ sudo /usr/bin/perl install-module.pl --all
Checking for CPAN (v1.81) ok: found v2.10
Checking for YAML (any) ok: found v1.15
Checking for ExtUtils-MakeMaker (v6.31) ok: found v7.1
defined(#array) is deprecated at /usr/share/perl5/Chart/Base.pm line 181.
(Maybe you should just omit the defined()?)
defined(#array) is deprecated at /usr/share/perl5/Chart/Base.pm line 233.
(Maybe you should just omit the defined()?)
Reading '/home/ubuntu/.cpan/Metadata'
Fetching with LWP:
http://cpan.mirror.vexxhost.com/authors/01mailrc.txt.gz
Reading '/home/ubuntu/.cpan/source/authors/01mailrc.txt.gz'
............................................................................DONE
Fetching with LWP:
http://cpan.mirror.vexxhost.com/modules/02packages.details.txt.gz
Reading '/home/ubuntu/.cpan/source/modules/02packages.details.txt.gz'
Database was generated on Wed, 30 Sep 2015 09:53:42 GMT
..........ubuntu#ip-10-130-10-107:/srv/www/bugzilla$
I'm not sure why things just don't work for me. Do I have a faulty perl installation or what? Can some perl guru please help?
Thanks!
Solved the issue by killing my Bugzilla installation (5.0.1) and completely re-install an older version (4.4.10). Things just worked with the previous version.
I fought with the same problem, with Bugzilla 5, for half a day. I did not have any success getting STARTTLS to work, which is odd, because it's the standard way to send email these days. I finally gave up and activated SMTPS (port 465) on my Postfix server. It was very easy to do this, and once I did it, Bugzilla could send emails easily. If you have control over the mail server, this is an easier approach because life is too short to spend it reading through perl code. Edit: all these years later, STARTTLS still doesn't work on Bugzilla. I tried installing libnet-smtp-tls-butmaintained-perl which some suggested, but that didn't help. For those finding this post, give up and use smtps.
If I have warn statements in my code, and I run this code normally from the command line, I see the warning message on the console. Similarly if I run this code under Apache my warn message appears in Apache's error log.
If I run the same code under perl -d, I see a stack dump every time I execute a warning. The same thing happens when my code passes through an active Smart::Comments. Can I do anything about this?
Example:
DB<8>
Highway::eBookGenerator::build(/var/www/highway/app/Highway/eBookGenerator.pm:133):
133: $self->{opts}->{debug} = '' unless $self->{opts}->{debug};
DB<8>
Highway::eBookGenerator::build(/var/www/highway/app/Highway/eBookGenerator.pm:135):
135: warn "build IS RUNNING UNSTABLE" if $self->{opts}->{runningunstable};
DB<8>
build IS RUNNING UNSTABLE at /var/www/highway/app/Highway/eBookGenerator.pm line 135.
at /var/www/highway/app/Highway/eBookGenerator.pm line 135.
Highway::eBookGenerator::build('Highway::eBookGenerator=HASH(0xf2da4f0)', 'HASH(0xf1369e8)') called at /var/www/highway/app//Highway/Page/eBookViewer.pm line 2448
Highway::Page::eBookViewer::create_epub_process('Highway::Page::eBookViewer=HASH(0xf35b038)') called at /var/www/highway/app/_cpan/CGI/Application.pm line 157
eval {...} called at /var/www/highway/app/_cpan/CGI/Application.pm line 156
CGI::Application::__get_body('Highway::Page::eBookViewer=HASH(0xf35b038)', 'create_epub_process') called at /var/www/highway/app/_cpan/CGI/Application.pm line 234
.... yada yada 20 lines of stack dump
Test::WWW::Mechanize::post_ok('Test::WWW::Mechanize::PSGI=HASH(0xea5d230)', '/ebooks/create_epub_process', 'HASH(0x159f8d0)') called at t/ebookGenTest.pl line 160
Highway::eBookGenerator::build(/var/www/highway/app/Highway/eBookGenerator.pm:140):
Putting:
$SIG{__WARN__} = sub { };
in your main source file should catch and thus suppress any future warnings. Or you can do:
$SIG{__WARN__} = sub { print "$1\n" if $1 };
to have a non-intrusive message.
I am building an application on Catalyst framework and I am a complete novice at it. Yesterday I installed SQLite and since then I am getting error messages like:
mohit#mohit-Studio-1555:~$ catalyst.pl
Undefined subroutine &Catalyst::Exception::Base::with called at /usr/share/perl5/Catalyst/Exception.pm line 50.
Compilation failed in require at /usr/share/perl5/Catalyst/Utils.pm line 4.
BEGIN failed--compilation aborted at /usr/share/perl5/Catalyst/Utils.pm line 4.
Compilation failed in require at /usr/share/perl5/Catalyst/Helper.pm line 12.
BEGIN failed--compilation aborted at /usr/share/perl5/Catalyst/Helper.pm line 12.
Compilation failed in require at /usr/bin/catalyst.pl line 26.
BEGIN failed--compilation aborted at /usr/bin/catalyst.pl line 26.
I tried reinstalling, cleaning and tried to google it but unable to resolve.
Please help me out. What can be the problem?
After upgrading namespace::clean I get this error:
The old Moose::Util::MetaRole API (before version 0.94) has been deprecated at /usr/share/perl5/Catalyst/Exception/Basic.pm line 3
Catalyst::Exception::Basic::BEGIN() called at /usr/lib/perl5/MooseX/Role/WithOverloading.pm line 3
eval {...} called at /usr/lib/perl5/MooseX/Role/WithOverloading.pm line 3
require Catalyst/Exception/Basic.pm called at /usr/local/lib/perl/5.10.1/Class/MOP.pm line 114
Class::MOP::__ANON__() called at /usr/local/share/perl/5.10.1/Try/Tiny.pm line 71
eval {...} called at /usr/local/share/perl/5.10.1/Try/Tiny.pm line 67
Try::Tiny::try('CODE(0x8f366b8)', 'Try::Tiny::Catch=REF(0x8e6b9c8)') called at /usr/local/lib/perl/5.10.1/Class/MOP.pm line 125
Class::MOP::load_first_existing_class('Catalyst::Exception::Basic') called at /usr/local/lib/perl/5.10.1/Class/MOP.pm line 137
Class::MOP::load_class('Catalyst::Exception::Basic', undef) called at /usr/local/lib/perl/5.10.1/Moose/Util.pm line 113
Moose::Util::_apply_all_roles('Moose::Meta::Class=HASH(0x8f36458)', undef, 'Catalyst::Exception::Basic') called at /usr/local/lib/perl/5.10.1/Moose/Util.pm line 91
It looks like you installed a version of Package::Stash which breaks your installed version of namespace::clean and didn't catch the conflict warning. Upgrading namespace::clean to the newest version should resolve your problems.