{"action":"created","issue":{"url":"https://api.github.com/repos/Rostlab/SNAP2/issues/4","labels_url":"https://api.github.com/repos/Rostlab/SNAP2/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/Rostlab/SNAP2/issues/4/comments","events_url":"https://api.github.com/repos/Rostlab/SNAP2/issues/4/events","html_url":"https://github.com/Rostlab/SNAP2/issues/4","id":118752997,"number":4,"title":"runtime error of snap2","user":{"login":"seitza","id":2892656,"avatar_url":"https://avatars.githubusercontent.com/u/2892656?v=3","gravatar_id":"","url":"https://api.github.com/users/seitza","html_url":"https://github.com/seitza","followers_url":"https://api.github.com/users/seitza/followers","following_url":"https://api.github.com/users/seitza/following{/other_user}","gists_url":"https://api.github.com/users/seitza/gists{/gist_id}","starred_url":"https://api.github.com/users/seitza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seitza/subscriptions","organizations_url":"https://api.github.com/users/seitza/orgs","repos_url":"https://api.github.com/users/seitza/repos","events_url":"https://api.github.com/users/seitza/events{/privacy}","received_events_url":"https://api.github.com/users/seitza/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"jmcejuela","id":102431,"avatar_url":"https://avatars.githubusercontent.com/u/102431?v=3","gravatar_id":"","url":"https://api.github.com/users/jmcejuela","html_url":"https://github.com/jmcejuela","followers_url":"https://api.github.com/users/jmcejuela/followers","following_url":"https://api.github.com/users/jmcejuela/following{/other_user}","gists_url":"https://api.github.com/users/jmcejuela/gists{/gist_id}","starred_url":"https://api.github.com/users/jmcejuela/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmcejuela/subscriptions","organizations_url":"https://api.github.com/users/jmcejuela/orgs","repos_url":"https://api.github.com/users/jmcejuela/repos","events_url":"https://api.github.com/users/jmcejuela/events{/privacy}","received_events_url":"https://api.github.com/users/jmcejuela/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/Rostlab/SNAP2/milestones/5","html_url":"https://github.com/Rostlab/SNAP2/milestones/2-ThisWeek","labels_url":"https://api.github.com/repos/Rostlab/SNAP2/milestones/5/labels","id":1509084,"number":5,"title":"2-ThisWeek","description":null,"creator":{"login":"jmcejuela","id":102431,"avatar_url":"https://avatars.githubusercontent.com/u/102431?v=3","gravatar_id":"","url":"https://api.github.com/users/jmcejuela","html_url":"https://github.com/jmcejuela","followers_url":"https://api.github.com/users/jmcejuela/followers","following_url":"https://api.github.com/users/jmcejuela/following{/other_user}","gists_url":"https://api.github.com/users/jmcejuela/gists{/gist_id}","starred_url":"https://api.github.com/users/jmcejuela/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmcejuela/subscriptions","organizations_url":"https://api.github.com/users/jmcejuela/orgs","repos_url":"https://api.github.com/users/jmcejuela/repos","events_url":"https://api.github.com/users/jmcejuela/events{/privacy}","received_events_url":"https://api.github.com/users/jmcejuela/received_events","type":"User","site_admin":false},"open_issues":1,"closed_issues":0,"state":"open","created_at":"2016-01-15T15:04:50Z","updated_at":"2016-01-15T15:04:50Z","due_on":null,"closed_at":null},"comments":10,"created_at":"2015-11-25T03:32:24Z","updated_at":"2016-01-18T12:35:47Z","closed_at":null,"body":"After finally having installed the tool, now running it fails. First I edited the config file in `~/.snap2rc`:\r\n\r\n```\r\n[snap2]\r\n# snapfun_utildir=path - path to package utilities, default: /usr/share/snap2\r\nsnap2dir=/usr/share/snap2\r\n#use snap cache [0|1], default: 0\r\nuse_snap_cache=0\r\n#snap cache fetch executable\r\nsnapc_fetch=/usr/bin/snapc_fetch\r\n#snap cache store executable\r\nsnapc_store=/usr/bin/snapc_store\r\n#snap cache root - overrides snap-cache-mgr configuration\r\nsnap_cache_root=\r\n# blastpgp_processors\r\nblastpgp_processors=1\r\n#use predictprotein cache, default: 0\r\nuse_pp_cache=0\r\n#predictprotein executable\r\npp_exe=/usr/bin/predictprotein\r\n#sift executable\r\nsift_exe=/usr/bin/sift_for_submitting_fasta_seq.csh\r\n#reprof executable\r\nreprof_exe=/usr/bin/reprof\r\n#blast executable\r\nblast_exe=/usr/bin/blastpgp\r\n\r\n\r\n[data]\r\n# swiss_dat=path - location of UniProt/Swiss-Prot dat file\r\nswiss_dat=/home/vagrant/snap_db_mnt/uniprot_sprot.dat\r\n# db_swiss=path - path to ID index of Swiss-Prot dat file (generated by /usr/share/librg-utils-perl/dbSwiss.pl)\r\ndb_swiss=/home/vagrant/snap_db_mnt/dbswiss\r\n# PHAT substitution matrix\r\nphat_matrix=/usr/share/snap2/phat.txt\r\n\r\n[blast]\r\n# big80=path - path to redundancy reduced database (UniProtKB 80 or equivalent)\r\nbig80=/home/vagrant/snap_db_mnt/uniref90.fasta\r\n# swiss=path - path to SwissProt database\r\nswiss=/home/vagrant/snap_db_mnt/uniprot_sprot.fasta\r\n```\r\n\r\nPlease note the last lines concerning `$big80` and `$swiss`, which I regard as the cause for the error. The rest of the config is default. I tried to enter only the path, the path to the original fast file, a path containing a wildcard to all files, which were generated by `makeblastdb`, and all single files, which were created by `makeblastdb`. All runs failed and result in the following error:\r\n\r\n```\r\n$ snap2 --seq AAAAAAAAAAAAAAAAA --cmdmuts A10S -o ~/test\r\nWorking directory: /tmp/8U7BA0jRh9\r\nJob name: test\r\n\r\nRunning external programs..\r\n*** ERROR blastpgp_to_saf.pl : *** ERROR blastp_to_saf: blast file format not recognized\r\nDied at /usr/share/librg-utils-perl//blastpgp_to_saf.pl line 76.\r\nmake: *** [query.safBlastPsi80] Error 255\r\nmake --no-builtin-rules INFILE=query.in -C /tmp/DSXzkuyD2k JOBID=query -j 1 BLASTCORES=1 LIBRGUTILS=/usr/share/librg-utils-perl/ PPROOT=/usr/share/predictprotein/ PROFNUMRESMIN=17 PROFROOT=/usr/share/profphd/prof/ BIGBLASTDB=/mnt/project/rost_db/data/blast/big BIG80BLASTDB=/mnt/project/rost_db/data/blast/big_80 PFAM2DB=/mnt/project/rost_db/data/pfam/Pfam_ls PFAM3DB=/mnt/project/rost_db/data/pfam/Pfam-A.hmm PROSITEDAT=/mnt/project/rost_db/data/prosite/prosite.dat PROSITECONVDAT=/mnt/project/rost_db/data/prosite/prosite_convert.dat PSICEXE=/usr/share/rost-runpsic/runNewPSIC.pl SPKEYIDX=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt SWISSBLASTDB=/mnt/project/rost_db/data/blast/swiss --quiet -f /usr/share/predictprotein/MakefilePP.mk query.mdisorder query.profRdb query.prof1Rdb query.profbval query.blastPsiMat query.isis query.clustalngz query.psic failed: 512 at /usr/bin/predictprotein line 391.\r\nFailed to execute '/usr/bin/predictprotein --seqfile=/tmp/8U7BA0jRh9/test.fasta --target=query.blastPsiMat --target=query.psic --target=query.profRdb --target=query.prof1Rdb --target=query.profbval --target=query.isis --target=query.mdisorder --target=query.clustalngz --blast-processors=1 --output-dir=/tmp/8U7BA0jRh9': 25 at /usr/share/perl5/RG/Snap2/Run.pm line 114\r\n\tRG::Snap2::Run::predictprotein('/tmp/8U7BA0jRh9', '/tmp/8U7BA0jRh9/test.fasta', undef, 1, 'test', undef, 0, '/usr/bin/predictprotein', 0, ...) called at /usr/share/perl5/RG/Snap2/Run.pm line 14\r\n\tRG::Snap2::Run::all('/tmp/8U7BA0jRh9/test.muts', '/tmp/8U7BA0jRh9', '/usr/bin/sift_for_submitting_fasta_seq.csh', '/home/vagrant/snap_db_mnt/uniref90.fasta.', '/home/vagrant/snap_db_mnt/uniprot_sprot.fasta', '/usr/bin/blastpgp', undef, 1, 'test', ...) called at /usr/share/perl5/RG/Snap2/Snap2.pm line 223\r\n\tRG::Snap2::Snap2::run('HASH(0x14ea2a0)', 1.0.10) called at /usr/bin/snap2 line 117\r\n```\r\n\r\nA very short personal meeting with @hechtm revealed a a potential problem (using the longest common suffix of all `makeblastdb`-generated files as input path), but didn't help so far. Anyone any ideas?"},"comment":{"url":"https://api.github.com/repos/Rostlab/SNAP2/issues/comments/172517209","html_url":"https://github.com/Rostlab/SNAP2/issues/4#issuecomment-172517209","issue_url":"https://api.github.com/repos/Rostlab/SNAP2/issues/4","id":172517209,"user":{"login":"seitza","id":2892656,"avatar_url":"https://avatars.githubusercontent.com/u/2892656?v=3","gravatar_id":"","url":"https://api.github.com/users/seitza","html_url":"https://github.com/seitza","followers_url":"https://api.github.com/users/seitza/followers","following_url":"https://api.github.com/users/seitza/following{/other_user}","gists_url":"https://api.github.com/users/seitza/gists{/gist_id}","starred_url":"https://api.github.com/users/seitza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seitza/subscriptions","organizations_url":"https://api.github.com/users/seitza/orgs","repos_url":"https://api.github.com/users/seitza/repos","events_url":"https://api.github.com/users/seitza/events{/privacy}","received_events_url":"https://api.github.com/users/seitza/received_events","type":"User","site_admin":false},"created_at":"2016-01-18T12:35:46Z","updated_at":"2016-01-18T12:35:46Z","body":"Hi @jmcejuela here's the Vagrantfile, I use. Please note, that there are some absolute paths, which require to be changed, before it can be used on another machine.\r\n[Vagrantfile.txt](https://github.com/Rostlab/SNAP2/files/94284/Vagrantfile.txt)\r\n\r\n"}}