{"action":"created","issue":{"url":"https://api.github.com/repos/sestaton/Transposome/issues/30","labels_url":"https://api.github.com/repos/sestaton/Transposome/issues/30/labels{/name}","comments_url":"https://api.github.com/repos/sestaton/Transposome/issues/30/comments","events_url":"https://api.github.com/repos/sestaton/Transposome/issues/30/events","html_url":"https://github.com/sestaton/Transposome/issues/30","id":104844762,"number":30,"title":"Can't locate error. Somewhere around a shell script at the beginning of Blast?","user":{"login":"RubyDrus","id":2803181,"avatar_url":"https://avatars.githubusercontent.com/u/2803181?v=3","gravatar_id":"","url":"https://api.github.com/users/RubyDrus","html_url":"https://github.com/RubyDrus","followers_url":"https://api.github.com/users/RubyDrus/followers","following_url":"https://api.github.com/users/RubyDrus/following{/other_user}","gists_url":"https://api.github.com/users/RubyDrus/gists{/gist_id}","starred_url":"https://api.github.com/users/RubyDrus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RubyDrus/subscriptions","organizations_url":"https://api.github.com/users/RubyDrus/orgs","repos_url":"https://api.github.com/users/RubyDrus/repos","events_url":"https://api.github.com/users/RubyDrus/events{/privacy}","received_events_url":"https://api.github.com/users/RubyDrus/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-09-04T07:50:55Z","updated_at":"2015-09-10T19:36:18Z","closed_at":null,"body":"Hi all,\r\n\r\njust started using Transposome but it fails right after starting it. I'm sorry I can't describe it better but there seems to be no verbose option. Here is the error message printed on screen (I have shortened some paths for clarity reasons):\r\n\r\n```\r\nINFO - ======== Transposome version: 0.09.8 (started at: 04-09-2015 09:29:55) ========\r\nINFO - Configuration - Log file for monitoring progress and errors: 2015-09-02_t_log.txt\r\nINFO - Configuration - Sequence file: ./data/2015-09-02_transposome/test_4100314/test_4100314.fastq\r\nINFO - Configuration - Sequence format: fastq\r\nINFO - Configuration - Sequence number for each BLAST process: 50000\r\nINFO - Configuration - Number of CPUs per thread: 1\r\nINFO - Configuration - Number of threads: 2\r\nINFO - Configuration - Output directory: ./data/2015-09-02_transposome/test_4100314/transposome_out\r\nINFO - Configuration - In-memory analysis:  1\r\nINFO - Configuration - Percent identity for matches: 90\r\nINFO - Configuration - Fraction coverage for pairwise matches: 0.55\r\nINFO - Configuration - Merge threshold for clusters: 0.001\r\nINFO - Configuration - Minimum cluster size for annotation: 100\r\nINFO - Configuration - BLAST e-value threshold for annotation: 10\r\nINFO - Configuration - Repeat database for annotation: ./data/genomic_dbs/2015-06-19_element_specific_sequences/repbase_homosapiens_alu_family.fasta\r\nINFO - Configuration - Log file for clustering/merging results: 2015-09-02_t_cluster_report.txt\r\nINFO - Transposome::Run::Blast::run_allvall_blast started at: 04-09-2015 09:29:56.\r\nsh: - : invalid option\r\nUsage:  sh [GNU long option] [option] ...\r\n        sh [GNU long option] [option] script-file ...\r\nGNU long options:\r\n        --debug\r\n        --debugger\r\n        --dump-po-strings\r\n        --dump-strings\r\n        --help\r\n        --init-file\r\n        --login\r\n        --import-functions\r\n        --noediting\r\n        --noprofile\r\n        --norc\r\n        --posix\r\n        --protected\r\n        --rcfile\r\n        --restricted\r\n        --verbose\r\n        --version\r\nShell options:\r\n        -irsD or -c command or -O shopt_option          (invocation only)\r\n        -abefhkmnptuvxBCHP or -o option\r\nUse of uninitialized value $mgblast in concatenation (.) or string at /ibios/tbi_cluster/11.4/x86_64/perl/perl-5.14.1/lib/site_perl/5.14.1/Transposome/Run/Blast.pm line 329.\r\nUse of uninitialized value $mgblast in concatenation (.) or string at /ibios/tbi_cluster/11.4/x86_64/perl/perl-5.14.1/lib/site_perl/5.14.1/Transposome/Run/Blast.pm line 329.\r\nsh: - : invalid option\r\nUsage:  sh [GNU long option] [option] ...\r\n        sh [GNU long option] [option] script-file ...\r\nGNU long options:\r\n        --debug\r\n        --debugger\r\n        --dump-po-strings\r\n        --dump-strings\r\n        --help\r\n        --init-file\r\n        --login\r\n        --import-functions\r\n        --noediting\r\n        --noprofile\r\n        --norc\r\n        --posix\r\n        --protected\r\n        --rcfile\r\n        --restricted\r\n        --verbose\r\n        --version\r\nShell options:\r\n        -irsD or -c command or -O shopt_option          (invocation only)\r\n        -abefhkmnptuvxBCHP or -o option\r\nsh: - : invalid option\r\nUsage:  sh [GNU long option] [option] ...\r\n        sh [GNU long option] [option] script-file ...\r\nGNU long options:\r\n        --debug\r\n        --debugger\r\n        --dump-po-strings\r\n        --dump-strings\r\n        --help\r\n        --init-file\r\n        --login\r\n        --import-functions\r\n        --noediting\r\n        --noprofile\r\n        --norc\r\n        --posix\r\n        --protected\r\n        --rcfile\r\n        --restricted\r\n        --verbose\r\n        --version\r\nShell options:\r\n        -irsD or -c command or -O shopt_option          (invocation only)\r\n        -abefhkmnptuvxBCHP or -o option\r\n\r\n[ERROR]: Could not open file: ./data/2015-09-02_transposome/test_4100314/transposome_out/test_4100314_2_yUqu_test_4100314_allvall_mgblastdb.bln\r\n```\r\nOne thing seems to stand out: The name of the file it could not find looks different from the actual file it is searching for:\r\n\r\nFrom the screen:\r\n./data/2015-09-02_transposome/test_4100314/transposome_out/**test_4100314_2_yUqu_test_4100314_allvall_mgblastdb.bln**\r\n\r\nCompared to the actual but empty file named:\r\n./data/2015-09-02_transposome/test_4100314/transposome_out/test_4100314_allvall_blast.bln\r\n\r\nSince it probably cannot start blast as wished, I assumed that our customised cluster architecture might a problem. So I tried several combinations of alias for blast like `alias blast=\"blastn\"` or `alias mgblast=\"mgblast-0.09.8\"` but that didn't help.\r\n\r\nThank you in advance!\r\n\r\nAll the best,\r\nRuben\r\n\r\nEdit: Maybe I should mention that I only use 100,000 reads of a sample which contains 67m reads in total."},"comment":{"url":"https://api.github.com/repos/sestaton/Transposome/issues/comments/139355716","html_url":"https://github.com/sestaton/Transposome/issues/30#issuecomment-139355716","issue_url":"https://api.github.com/repos/sestaton/Transposome/issues/30","id":139355716,"user":{"login":"sestaton","id":1477856,"avatar_url":"https://avatars.githubusercontent.com/u/1477856?v=3","gravatar_id":"","url":"https://api.github.com/users/sestaton","html_url":"https://github.com/sestaton","followers_url":"https://api.github.com/users/sestaton/followers","following_url":"https://api.github.com/users/sestaton/following{/other_user}","gists_url":"https://api.github.com/users/sestaton/gists{/gist_id}","starred_url":"https://api.github.com/users/sestaton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sestaton/subscriptions","organizations_url":"https://api.github.com/users/sestaton/orgs","repos_url":"https://api.github.com/users/sestaton/repos","events_url":"https://api.github.com/users/sestaton/events{/privacy}","received_events_url":"https://api.github.com/users/sestaton/received_events","type":"User","site_admin":false},"created_at":"2015-09-10T19:36:18Z","updated_at":"2015-09-10T19:36:18Z","body":"The last step should be:\r\n\r\n    sudo make install\r\n\r\nand that would have installed the programs, but I assume that did that. Unfortunately, I don't have an openSUSE machine to test nor can I find that available from the cloud services I use. I don't know what to offer at this point since I can't see the output of any of those steps to see what went wrong. One issue I have had in the past is the Admins setting a PATH and the PERL5LIB variable for all users and this interferes with some applications. \r\n\r\nTo avoid these issues, I would recommend setting up [perlbrew](http://perlbrew.pl/) and installing Transposome yourself. This tool (perlbrew) will install Perl in your home directory, then you can install anything you want without admin privileges (there are other benefits too). The whole process would look like this:\r\n\r\n    \\curl -L http://install.perlbrew.pl | bash\r\n    echo \"source ~/perl5/perlbrew/etc/bashrc\" >> ~/.bashrc\r\n    source ~/.bashrc\r\n    perlbrew install perl-5.20.0 -Dusethreads\r\n    perlbrew switch perl-5.22.0\r\n    perlbrew install-cpanm\r\n\r\nThen, you should be able to install Transposome with one command:\r\n\r\n    cpanm git://github.com/sestaton/Transposome.git\r\n\r\nOf course, a couple of these steps take some time (installing Perl, then Transposome), but this will create a log of steps where I can see any issues, if there are any. As an aside, this is how I use Perl and Transposome."}}