{"action":"created","issue":{"url":"https://api.github.com/repos/stamatak/standard-RAxML/issues/32","repository_url":"https://api.github.com/repos/stamatak/standard-RAxML","labels_url":"https://api.github.com/repos/stamatak/standard-RAxML/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/stamatak/standard-RAxML/issues/32/comments","events_url":"https://api.github.com/repos/stamatak/standard-RAxML/issues/32/events","html_url":"https://github.com/stamatak/standard-RAxML/issues/32","id":139594239,"number":32,"title":"Core dumped when adding bipartition information to a tree","user":{"login":"jgerken","id":1132816,"avatar_url":"https://avatars.githubusercontent.com/u/1132816?v=3","gravatar_id":"","url":"https://api.github.com/users/jgerken","html_url":"https://github.com/jgerken","followers_url":"https://api.github.com/users/jgerken/followers","following_url":"https://api.github.com/users/jgerken/following{/other_user}","gists_url":"https://api.github.com/users/jgerken/gists{/gist_id}","starred_url":"https://api.github.com/users/jgerken/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jgerken/subscriptions","organizations_url":"https://api.github.com/users/jgerken/orgs","repos_url":"https://api.github.com/users/jgerken/repos","events_url":"https://api.github.com/users/jgerken/events{/privacy}","received_events_url":"https://api.github.com/users/jgerken/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-03-09T14:40:08Z","updated_at":"2016-03-09T18:09:49Z","closed_at":null,"body":"I have calculated a tree using the following command (the alignment was checked previously):\r\n\r\n```\r\nraxmlHPC-PTHREADS-AVX2 -D -f D -F -j -m GTRCAT -n NAME -O -p 28759 -s alignment.fasta -T 4 --silent --no-seq-check\r\n```\r\n\r\nthan I ran the following command to add the RELL bootstrap information to the result tree:\r\n\r\n```\r\nraxmlHPC-PTHREADS-AVX2 -f b -j -m GTRCAT -n NAME-BS -t RAxML_result.NAME -T 4 -z RAxML_rellBootstrap.NAME\r\n```\r\n\r\nThis command fails with the following message:\r\n\r\n```\r\nraxmlHPC-PTHREADS-AVX2: treeIO.c:1397: treeReadLen: Assertion `0' failed.\r\n/var/spool/gridengine/execd/mg9/job_scripts/645420: line 21: 24614 Aborted                 (core dumped) \"${RAXML}\" ${PARAMS} $1\r\n```\r\n\r\nSince I skipped the GAMMA optimization and did not run the `-f e` command (would have been run with GTRCAT, too) my tree has no branch lengths yet. Could that be the problem? It would be great if RAxML gives an error message pointing to the problem\u0010.\r\n\r\nI have the core file (29G) and the tree files (4.9M and 4.8G) but I cannot attach them here due to their size (the tree has 279,954 sequences/taxa). Send me a message if you need them for debugging, I will then setup a download option for you."},"comment":{"url":"https://api.github.com/repos/stamatak/standard-RAxML/issues/comments/194429634","html_url":"https://github.com/stamatak/standard-RAxML/issues/32#issuecomment-194429634","issue_url":"https://api.github.com/repos/stamatak/standard-RAxML/issues/32","id":194429634,"user":{"login":"jgerken","id":1132816,"avatar_url":"https://avatars.githubusercontent.com/u/1132816?v=3","gravatar_id":"","url":"https://api.github.com/users/jgerken","html_url":"https://github.com/jgerken","followers_url":"https://api.github.com/users/jgerken/followers","following_url":"https://api.github.com/users/jgerken/following{/other_user}","gists_url":"https://api.github.com/users/jgerken/gists{/gist_id}","starred_url":"https://api.github.com/users/jgerken/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jgerken/subscriptions","organizations_url":"https://api.github.com/users/jgerken/orgs","repos_url":"https://api.github.com/users/jgerken/repos","events_url":"https://api.github.com/users/jgerken/events{/privacy}","received_events_url":"https://api.github.com/users/jgerken/received_events","type":"User","site_admin":false},"created_at":"2016-03-09T18:09:49Z","updated_at":"2016-03-09T18:09:49Z","body":"Now further calculations has finished and I can confirm when running the `-f e`command prior to the `-f b`, the tree containing the bi-partition information is created successfully. Thus, the easiest solution will likely be to insert a check for the presence of the branch lengths, giving an appropriate error message if they are missing and add the prerequisite to the manual. \r\n\r\nHowever, I do not unterstand why adding the bi-partition information to the tree requires the branch lengths. In my opinion, both operations are complete unrelated."}}