{"action":"created","issue":{"url":"https://api.github.com/repos/soedinglab/mmseqs2/issues/3","repository_url":"https://api.github.com/repos/soedinglab/mmseqs2","labels_url":"https://api.github.com/repos/soedinglab/mmseqs2/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/soedinglab/mmseqs2/issues/3/comments","events_url":"https://api.github.com/repos/soedinglab/mmseqs2/issues/3/events","html_url":"https://github.com/soedinglab/mmseqs2/issues/3","id":179975964,"number":3,"title":"Core dumping during \"createindex\"","user":{"login":"hingamp","id":12284507,"avatar_url":"https://avatars.githubusercontent.com/u/12284507?v=3","gravatar_id":"","url":"https://api.github.com/users/hingamp","html_url":"https://github.com/hingamp","followers_url":"https://api.github.com/users/hingamp/followers","following_url":"https://api.github.com/users/hingamp/following{/other_user}","gists_url":"https://api.github.com/users/hingamp/gists{/gist_id}","starred_url":"https://api.github.com/users/hingamp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hingamp/subscriptions","organizations_url":"https://api.github.com/users/hingamp/orgs","repos_url":"https://api.github.com/users/hingamp/repos","events_url":"https://api.github.com/users/hingamp/events{/privacy}","received_events_url":"https://api.github.com/users/hingamp/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-09-29T07:49:30Z","updated_at":"2016-10-04T07:47:47Z","closed_at":null,"body":"Hello,\r\nI'm eager to try mmseqs but have been unsuccessful at building the database for UniRef90, as mmseqs seg faults and core dumps during the \"createindex\" phase. I tried both the precompiled mmseqs and my own compiled version, without --split or --threads, as well as with various combinations of both --split and --threads. My machine has 128 GB RAM (and same size swap space) and 6TB free space on hard drive. The process dies before ever reaching more than 40% of RAM. The output is:\r\n\r\n```bash\r\nmmseqs createdb  uniref90/uniref90.fasta uniref90.mms\r\n\r\nls -ltr uniref90/\r\n-rw-r--r-- 1 hingamp.p MIO 19965315337 sept. 28 22:51 uniref90.fasta\r\n-rw-r--r-- 1 hingamp.p MIO  1244574423 sept. 29 00:07 uniref90.mms.lookup\r\n-rw-r--r-- 1 hingamp.p MIO  4652608129 sept. 29 00:07 uniref90.mms_h\r\n-rw-r--r-- 1 hingamp.p MIO  1025056829 sept. 29 00:09 uniref90.mms_h.index\r\n-rw-r--r-- 1 hingamp.p MIO 15172645206 sept. 29 00:09 uniref90.mms\r\n-rw-r--r-- 1 hingamp.p MIO  1063262010 sept. 29 00:11 uniref90.mms.index\r\n\r\nmmseqs createindex uniref90/uniref90.mms --split 10 --threads 20\r\nProgram call:\r\nuniref90/uniref90.mms --split 10 --threads 20 \r\n\r\nMMseqs Version:     \tab6d7b3105611a0860c801603997f1721785916a\r\nSub Matrix          \tblosum62.out\r\nK-mer size          \t0\r\nAlphabet size       \t21\r\nmax. sequence length\t32000\r\nSplit DB            \t10\r\nspaced Kmer         \t1\r\nThreads             \t20\r\nVerbosity           \t3\r\n\r\nSubstitution matrices...\r\nIndex table: counting k-mers...\r\n.WARNING: Sequence (dbKey=10870) contains only ATGC. It might be a nucleotide sequence.\r\n..................................................................................................\t1 Mio. sequences processed\r\n...................................................................................................\t2 Mio. sequences processed\r\n...................................................................................................\t3 Mio. sequences processed\r\n...............................................................................\r\nIndex table: Masked residues: 26370434\r\nIndex table: fill...\r\n...................................................................................................\t1 Mio. sequences processed\r\n...................................................................................................\t2 Mio. sequences processed\r\n...................................................................................................\t3 Mio. sequences processed\r\n...............................................................................\r\nIndex table: removing duplicate entries...\r\nIndex table init done.\r\n\r\nWrite 10\r\nWrite 20\r\nWrite 60\r\nWrite 70\r\nWrite 80\r\nWrite 30\r\nWrite 40\r\nIndex table: counting k-mers...\r\n...................................................................................................\t1 Mio. sequences processed\r\n...........................................................................................WARNING: Sequence (dbKey=5712154) contains only ATGC. It might be a nucleotide sequence.\r\n........\t2 Mio. sequences processed\r\n...........................................................WARNING: Sequence (dbKey=6387662) contains only ATGC. It might be a nucleotide sequence.\r\n........................................\t3 Mio. sequences processed\r\n...................................................................\r\nIndex table: Masked residues: 47802947\r\nIndex table: fill...\r\nErreur de segmentation (core dumped)\r\n```\r\nMany thanks for any help or advice. I have watched the mmseqs demo on https://www.youtube.com/watch?v=LqiHyCLjPno and am looking forward to enjoying the huge simplification it promises (the last example in the demo is the 2bLCA we applied to metagenomics data and my workflow was much more complex and slow than with mmseqs!)...\r\nBest, \r\nPascal"},"comment":{"url":"https://api.github.com/repos/soedinglab/mmseqs2/issues/comments/251317885","html_url":"https://github.com/soedinglab/mmseqs2/issues/3#issuecomment-251317885","issue_url":"https://api.github.com/repos/soedinglab/mmseqs2/issues/3","id":251317885,"user":{"login":"martin-steinegger","id":1413571,"avatar_url":"https://avatars.githubusercontent.com/u/1413571?v=3","gravatar_id":"","url":"https://api.github.com/users/martin-steinegger","html_url":"https://github.com/martin-steinegger","followers_url":"https://api.github.com/users/martin-steinegger/followers","following_url":"https://api.github.com/users/martin-steinegger/following{/other_user}","gists_url":"https://api.github.com/users/martin-steinegger/gists{/gist_id}","starred_url":"https://api.github.com/users/martin-steinegger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martin-steinegger/subscriptions","organizations_url":"https://api.github.com/users/martin-steinegger/orgs","repos_url":"https://api.github.com/users/martin-steinegger/repos","events_url":"https://api.github.com/users/martin-steinegger/events{/privacy}","received_events_url":"https://api.github.com/users/martin-steinegger/received_events","type":"User","site_admin":false},"created_at":"2016-10-04T07:47:47Z","updated_at":"2016-10-04T07:47:47Z","body":"Did you inted to compile with MPI? Could you please send me your cmake call and output? \r\nIf you do not want to use MPI you can specify `cmake -DHAVE_MPI=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..`\r\n\r\nThe MPI compiled version can not be used as stand alone binary. You have to specificy an MPI runner and the amount of nodes you want to run your code. E.g. `RUNNER=\"mpirun -np 42\" mmseqs search queryDB targetDB resultDB tmp`. \r\n\r\nI also see that your query set has the size 0. `Query database: tara_test.faa(size=0)`. How did you build this query set? Could you please send us your workflow? "}}
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