{"action":"created","issue":{"url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/21","repository_url":"https://api.github.com/repos/PASApipeline/PASApipeline","labels_url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/21/comments","events_url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/21/events","html_url":"https://github.com/PASApipeline/PASApipeline/issues/21","id":166989893,"number":21,"title":"Error, cannot locate pasa binary","user":{"login":"wangzhennan14","id":17285718,"avatar_url":"https://avatars.githubusercontent.com/u/17285718?v=3","gravatar_id":"","url":"https://api.github.com/users/wangzhennan14","html_url":"https://github.com/wangzhennan14","followers_url":"https://api.github.com/users/wangzhennan14/followers","following_url":"https://api.github.com/users/wangzhennan14/following{/other_user}","gists_url":"https://api.github.com/users/wangzhennan14/gists{/gist_id}","starred_url":"https://api.github.com/users/wangzhennan14/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wangzhennan14/subscriptions","organizations_url":"https://api.github.com/users/wangzhennan14/orgs","repos_url":"https://api.github.com/users/wangzhennan14/repos","events_url":"https://api.github.com/users/wangzhennan14/events{/privacy}","received_events_url":"https://api.github.com/users/wangzhennan14/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-07-22T07:55:14Z","updated_at":"2016-07-23T06:00:23Z","closed_at":null,"body":"When I use the sample data to test PASA, there is an error, the command line I run is:\r\n./run_sample_pipeline.pl\r\n\r\nand the error is:\r\n\r\n## Processing CMD: 30/40\r\n23:31:35        CMD: /disk11/wangzhn/scorpion/software/PASApipeline-2.0.2/scripts/..//scripts/assemble_clusters.dbi -G genome_sample.fasta  -M sample_mydb_pasa  -T 2  > sample_mydb_pasa.pasa_alignment_assembly_building.ascii_illustrations.out\r\nError, cannot locate pasa binary.  at /disk11/wangzhn/scorpion/software/PASApipeline-2.0.2/scripts/..//scripts/assemble_clusters.dbi line 83.\r\n\r\n\r\nERROR: The following command died with exit code (256):\r\n/disk11/wangzhn/scorpion/software/PASApipeline-2.0.2/scripts/..//scripts/assemble_clusters.dbi -G genome_sample.fasta  -M sample_mydb_pasa  -T 2  > sample_mydb_pasa.pasa_alignment_assembly_building.ascii_illustrations.out\r\n\r\nMust re-run pipeline starting at index [30] via running Launch_PASA_pipeline with parameter '-s 30' (exclude param '-C' since db already created)\r\n\r\nError, cmd: ../scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -r -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 2 -N 2 --TDN tdn.accs  --IMPORT_CUSTOM_ALIGNMENTS_GFF3 custom_alignments.gff3  died with ret(6400)  at ./run_sample_pipeline.pl line 186.\r\n\r\nCan you tell me how to solve this problem? Thank you."},"comment":{"url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/comments/234701602","html_url":"https://github.com/PASApipeline/PASApipeline/issues/21#issuecomment-234701602","issue_url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/21","id":234701602,"user":{"login":"wangzhennan14","id":17285718,"avatar_url":"https://avatars.githubusercontent.com/u/17285718?v=3","gravatar_id":"","url":"https://api.github.com/users/wangzhennan14","html_url":"https://github.com/wangzhennan14","followers_url":"https://api.github.com/users/wangzhennan14/followers","following_url":"https://api.github.com/users/wangzhennan14/following{/other_user}","gists_url":"https://api.github.com/users/wangzhennan14/gists{/gist_id}","starred_url":"https://api.github.com/users/wangzhennan14/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wangzhennan14/subscriptions","organizations_url":"https://api.github.com/users/wangzhennan14/orgs","repos_url":"https://api.github.com/users/wangzhennan14/repos","events_url":"https://api.github.com/users/wangzhennan14/events{/privacy}","received_events_url":"https://api.github.com/users/wangzhennan14/received_events","type":"User","site_admin":false},"created_at":"2016-07-23T06:00:23Z","updated_at":"2016-07-23T06:00:23Z","body":"dear brianjohnhaas,\r\n          \r\n        Thank you for your help, but when I use the sample data tu run ./run_sample_pipeline.pl, there is an error, and I can not understand.\r\n\r\n       ## Processing CMD:\r\n21:35:09        CMD: /disk11/wangzhn/scorpion/software/pasa/scripts/..//scripts/Load_Current_Gene_Annotations.dbi -c annotCompare.config -g genome_sample.fasta -P orig_annotations_sample.gff3  > pasa_run.log.dir/output.annot_loading.55579.out\r\nperl: symbol lookup error: /usr/local/bin/perl/site/lib/auto/DB_File/DB_File.so: undefined symbol: db_version\r\nUse of uninitialized value $index in concatenation (.) or string at ../scripts/Launch_PASA_pipeline.pl line 981.\r\nUse of uninitialized value $index in concatenation (.) or string at ../scripts/Launch_PASA_pipeline.pl line 981.\r\n\r\n\r\nERROR: The following command died with exit code (32512):\r\n/disk11/wangzhn/scorpion/software/pasa/scripts/..//scripts/Load_Current_Gene_Annotations.dbi -c annotCompare.config -g genome_sample.fasta -P orig_annotations_sample.gff3  > pasa_run.log.dir/output.annot_loading.55579.out\r\n\r\nMust re-run pipeline starting at index [] via running Launch_PASA_pipeline with parameter '-s ' (exclude param '-C' since db already created)\r\n\r\nError, cmd: ../scripts/Launch_PASA_pipeline.pl -c annotCompare.config -g genome_sample.fasta -t all_transcripts.fasta.clean -A -L --annots_gff3 orig_annotations_sample.gff3 --CPU 2 died with ret(32512)  at ./run_sample_pipeline.pl line 186.\r\n\r\n\r\n             I have read the output.annot_loading.55579.out, in this file , there is one message, I do not know what does it mean,\r\n\r\n             CMD: /disk11/wangzhn/scorpion/software/pasa/scripts/..//scripts/Annotation_store_preloader.dbi -c annotCompare.config\r\n\r\n\r\n             How to deal with this problem? Can you help me to solve it? Thank you!\r\n\r\n                                                                                                                                                                                                                                                                                                               wang"}}
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