{"action":"created","issue":{"url":"https://api.github.com/repos/epruesse/SINA/issues/53","repository_url":"https://api.github.com/repos/epruesse/SINA","labels_url":"https://api.github.com/repos/epruesse/SINA/issues/53/labels{/name}","comments_url":"https://api.github.com/repos/epruesse/SINA/issues/53/comments","events_url":"https://api.github.com/repos/epruesse/SINA/issues/53/events","html_url":"https://github.com/epruesse/SINA/issues/53","id":408420580,"node_id":"MDU6SXNzdWU0MDg0MjA1ODA=","number":53,"title":"Problem  regarding sina","user":{"login":"debjitde01","id":28703663,"node_id":"MDQ6VXNlcjI4NzAzNjYz","avatar_url":"https://avatars3.githubusercontent.com/u/28703663?v=4","gravatar_id":"","url":"https://api.github.com/users/debjitde01","html_url":"https://github.com/debjitde01","followers_url":"https://api.github.com/users/debjitde01/followers","following_url":"https://api.github.com/users/debjitde01/following{/other_user}","gists_url":"https://api.github.com/users/debjitde01/gists{/gist_id}","starred_url":"https://api.github.com/users/debjitde01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/debjitde01/subscriptions","organizations_url":"https://api.github.com/users/debjitde01/orgs","repos_url":"https://api.github.com/users/debjitde01/repos","events_url":"https://api.github.com/users/debjitde01/events{/privacy}","received_events_url":"https://api.github.com/users/debjitde01/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2019-02-09T10:54:46Z","updated_at":"2019-02-20T05:09:33Z","closed_at":null,"author_association":"NONE","body":"I am working with sina and this is the script which i have used it takes too much time still it is not complete. is it running ok?\r\n\r\n(sina) pkd@pkd-HP-406-G1-MT:~$ sina -i ~/Sina/amplicons_seeds.fasta --intype fasta -o sina_out --outtype fasta --search --meta-fmt csv --overhang remove --insertion forbid --filter none --fs-kmer-no-fast --fs-kmer-len 10 --fs-req 2 --fs-req-full 1 --fs-min 40 --fs-max 40 --fs-weight 1 --fs-full-len 350 --fs-msc 0.7 --match-score 1 --mismatch-score -1 --pen-gap 5 --pen-gapext 2 --search-cover query --search-iupac optimistic --search-min-sim 0.9 --turn all --lca-quorum 0.7 --search-db ~/Sina/sina_ssu.arb --db ~/Sina/sina_ssu.arb --lca-fields tax_slv\r\n[2019-02-09 13:54:08.891] [log] [info] Loglevel set to warning\r\n13:54:08 [SINA] This is SINA 1.4.0.\r\n\r\n0%   10   20   30   40   50   60   70   80   90   100%\r\n|----|----|----|----|----|----|----|----|----|----|\r\n***************************************************\r\nARB: Loading '/home/pkd/Sina/sina_ssu.arb.index.arb'\r\nARB: no FastLoad File '/home/pkd/Sina/sina_ssu.arb.index.ARM' found => loading entire DB\r\nARB: Loading '/home/pkd/Sina/sina_ssu.arb.index.arb' done\r\n\r\nProgress: Remove unused database entries\r\n...................................................................... [100.0%] used: 5s\r\n[done]\r\nDatabase contains 38792 species\r\nProgress: Preparing sequence data\r\n...................................................................... [100.0%] used: 4s\r\n[done]\r\n\r\nAll species contain data in alignment 'ali_16s'.\r\n[ptserver '-build_clean' took 10s]\r\nsum of above:  0 b\r\noverall alloc: 0 b\r\nsum of above:  0 b\r\noverall alloc: 0 b\r\nARB: Loading '/home/pkd/Sina/sina_ssu.arb.index.arb'\r\nARB: Opening FastLoad File '/home/pkd/Sina/sina_ssu.arb.index.ARM' ...\r\nARB: Loading '/home/pkd/Sina/sina_ssu.arb.index.arb' done\r\n\r\nBuilding PT-Server for alignment 'ali_16s'...\r\nDatabase contains 38792 species\r\nProgress: Checking data\r\n...................................................................... [100.0%] used: 0s\r\n[done]\r\nFailed to write to '/home/pkd/anaconda3/envs/sina/lib/arb/lib/pts/ptserver.log'\r\nVisible memory: 11.7 Gb\r\nRestricting used memory (by internal default '90%') to 10.5 Gb\r\nNote: Setting envar ARB_MEMORY will override that restriction (percentage or absolute memsize)\r\nMemory available for build: 10.4 Gb\r\nEstimated memory usage for 1 pass: 752 Mb\r\nOverall bases:       54.1 Mbp\r\nMax. partition size: 54.1 Mbp (=100.0%)\r\nProgress: Build index in 1 passes\r\n{pass 1/1}............................................................ [ 25.0%] left: 33s\r\n...................................................................... [ 50.0%] left: 25s\r\n...................................................................... [ 75.0%] left: 13s\r\n...................................................................... [100.0%] used: 1m0s\r\n[done]\r\nPT_SERVER database \"/home/pkd/Sina/sina_ssu.arb.index.arb\" has been created.\r\nFailed to write to '/home/pkd/anaconda3/envs/sina/lib/arb/lib/pts/ptserver.log'\r\n[ptserver '-build' took 1m2s]\r\narb_message: PT_SERVER database \"/home/pkd/Sina/sina_ssu.arb.index.arb\" has been created.\r\nblocksize:  9  allocated:  304 kb [~ 0%]  <~33.8 kBlocks [PT1_EMPTY_NODE_SIZE]\r\nblocksize: 10  allocated:  515 kb [~ 0%]  <~51.5 kBlocks\r\nblocksize: 11  allocated:  759 kb [~ 0%]  <~69.0 kBlocks [PT1_MIN_CHAIN_ENTRY_SIZE]\r\nblocksize: 12  allocated:  735 kb [~ 0%]  <~61.3 kBlocks\r\nblocksize: 13  allocated:  650 kb [~ 0%]  <~50.0 kBlocks\r\nblocksize: 14  allocated:  630 kb [~ 0%]  <~45.0 kBlocks\r\nblocksize: 15  allocated: 56.2 Mb [~11%]  <~3.75 MBlocks [PT1_EMPTY_LEAF_SIZE]\r\nblocksize: 16  allocated:  532 kb [~ 0%]  <~33.3 kBlocks\r\nblocksize: 17  allocated:  208 Mb [~41%]  <~12.3 MBlocks [PT1_NODE_WITHSONS_SIZE(1)]\r\nblocksize: 18  allocated:  477 kb [~ 0%]  <~26.6 kBlocks\r\nblocksize: 19  allocated:  451 kb [~ 0%]  <~23.8 kBlocks [PT1_CHAIN_SHORT_HEAD_SIZE]\r\nblocksize: 20  allocated:  415 kb [~ 0%]  <~20.8 kBlocks\r\nblocksize: 21  allocated:  389 kb [~ 0%]  <~18.6 kBlocks [PT1_CHAIN_LONG_HEAD_SIZE]\r\nblocksize: 22  allocated:  330 kb [~ 0%]  <~15.1 kBlocks\r\nblocksize: 23  allocated:  259 kb [~ 0%]  <~11.3 kBlocks [PT1_MAX_CHAIN_ENTRY_SIZE]\r\nblocksize: 24  allocated: 78.0 kb [~ 0%]  <~3.25 kBlocks\r\nblocksize: 25  allocated: 69.7 Mb [~14%]  <~2.79 MBlocks [PT1_NODE_WITHSONS_SIZE(2)]\r\nblocksize: 26  allocated:  221 kb [~ 0%]  <~8.51 kBlocks\r\nblocksize: 27  allocated:  385 kb [~ 0%]  <~14.3 kBlocks\r\nblocksize: 28  allocated:  539 kb [~ 0%]  <~19.3 kBlocks\r\nblocksize: 29  allocated: 14.6 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 30  allocated:  750 kb [~ 0%]  <~25.1 kBlocks\r\nblocksize: 31  allocated:  465 kb [~ 0%]  <~15.1 kBlocks\r\nblocksize: 32  allocated:  200 kb [~ 0%]  <~6.25 kBlocks\r\nblocksize: 33  allocated: 26.0 Mb [~ 5%]  <~ 807 kBlocks [PT1_NODE_WITHSONS_SIZE(3)]\r\nblocksize: 34  allocated: 8.51 kb [~ 0%]  <~  256 Blocks\r\nblocksize: 35  allocated:  403 kb [~ 0%]  <~11.6 kBlocks\r\nblocksize: 36  allocated:  630 kb [~ 0%]  <~17.6 kBlocks\r\nblocksize: 37  allocated:  204 kb [~ 0%]  <~5.50 kBlocks\r\nblocksize: 38  allocated:  266 kb [~ 0%]  <~7.00 kBlocks\r\nblocksize: 39  allocated: 9.76 kb [~ 0%]  <~  256 Blocks\r\nblocksize: 40  allocated:  520 kb [~ 0%]  <~13.1 kBlocks\r\nblocksize: 41  allocated:  113 Mb [~22%]  <~2.76 MBlocks [PT1_NODE_WITHSONS_SIZE(4)]\r\nblocksize: 42  allocated:  273 kb [~ 0%]  <~6.50 kBlocks\r\nblocksize: 43  allocated:  151 kb [~ 0%]  <~3.50 kBlocks\r\nblocksize: 44  allocated: 11.1 kb [~ 0%]  <~  256 Blocks\r\nblocksize: 45  allocated:  304 kb [~ 0%]  <~6.75 kBlocks\r\nblocksize: 46  allocated:  552 kb [~ 0%]  <~12.1 kBlocks\r\nblocksize: 47  allocated:  317 kb [~ 0%]  <~6.75 kBlocks\r\nblocksize: 48  allocated:  252 kb [~ 0%]  <~5.25 kBlocks\r\nblocksize: 49  allocated: 3.62 Mb [~ 1%]  <~75.5 kBlocks [PT1_NODE_WITHSONS_SIZE(5)]\r\nblocksize: 50  allocated:  113 kb [~ 0%]  <~2.25 kBlocks\r\nblocksize: 51  allocated:  179 kb [~ 0%]  <~3.50 kBlocks\r\nblocksize: 52  allocated:  312 kb [~ 0%]  <~6.00 kBlocks\r\nblocksize: 53  allocated:  199 kb [~ 0%]  <~3.75 kBlocks\r\nblocksize: 54  allocated: 13.6 kb [~ 0%]  <~  256 Blocks\r\nblocksize: 55  allocated:  206 kb [~ 0%]  <~3.75 kBlocks\r\nblocksize: 56  allocated: 98.0 kb [~ 0%]  <~1.75 kBlocks\r\nblocksize: 57  allocated:  941 kb [~ 0%]  <~16.6 kBlocks [PT1_NODE_WITHSONS_SIZE(6)]\r\nblocksize: 58  allocated:  479 kb [~ 0%]  <~8.26 kBlocks\r\nblocksize: 60  allocated:  450 kb [~ 0%]  <~7.50 kBlocks\r\nblocksize: 61  allocated:  290 kb [~ 0%]  <~4.75 kBlocks\r\nblocksize: 62  allocated: 93.0 kb [~ 0%]  <~1.50 kBlocks\r\nblocksize: 63  allocated: 63.0 kb [~ 0%]  <~1.00 kBlocks\r\nblocksize: 65  allocated:  146 kb [~ 0%]  <~2.25 kBlocks\r\nblocksize: 66  allocated:  215 kb [~ 0%]  <~3.25 kBlocks\r\nblocksize: 67  allocated:  251 kb [~ 0%]  <~3.75 kBlocks\r\nblocksize: 68  allocated:  136 kb [~ 0%]  <~2.00 kBlocks\r\nblocksize: 70  allocated:  140 kb [~ 0%]  <~2.00 kBlocks\r\nblocksize: 71  allocated:  142 kb [~ 0%]  <~2.00 kBlocks\r\nblocksize: 72  allocated:  180 kb [~ 0%]  <~2.50 kBlocks\r\nblocksize: 73  allocated:  383 kb [~ 0%]  <~5.25 kBlocks\r\nblocksize: 75  allocated:  206 kb [~ 0%]  <~2.75 kBlocks\r\nblocksize: 76  allocated:  209 kb [~ 0%]  <~2.75 kBlocks\r\nblocksize: 77  allocated:  366 kb [~ 0%]  <~4.75 kBlocks\r\nblocksize: 78  allocated:  176 kb [~ 0%]  <~2.25 kBlocks\r\nblocksize: 80  allocated: 80.0 kb [~ 0%]  <~1.00 kBlocks\r\nblocksize: 81  allocated: 40.5 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 82  allocated: 82.0 kb [~ 0%]  <~1.00 kBlocks\r\nblocksize: 83  allocated:  166 kb [~ 0%]  <~2.00 kBlocks\r\nblocksize: 85  allocated:  234 kb [~ 0%]  <~2.75 kBlocks\r\nblocksize: 86  allocated:  172 kb [~ 0%]  <~2.00 kBlocks\r\nblocksize: 87  allocated: 65.3 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 88  allocated: 88.0 kb [~ 0%]  <~1.00 kBlocks\r\nblocksize: 90  allocated:  158 kb [~ 0%]  <~1.75 kBlocks\r\nblocksize: 91  allocated:  159 kb [~ 0%]  <~1.75 kBlocks\r\nblocksize: 92  allocated:  322 kb [~ 0%]  <~3.50 kBlocks\r\nblocksize: 93  allocated:  186 kb [~ 0%]  <~2.00 kBlocks\r\nblocksize: 95  allocated:  143 kb [~ 0%]  <~1.50 kBlocks\r\nblocksize: 96  allocated:  240 kb [~ 0%]  <~2.50 kBlocks\r\nblocksize: 97  allocated:  291 kb [~ 0%]  <~3.00 kBlocks\r\nblocksize: 98  allocated:  221 kb [~ 0%]  <~2.25 kBlocks\r\nblocksize: 100  allocated: 75.0 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 101  allocated: 50.5 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 102  allocated: 51.0 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 103  allocated: 77.3 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 105  allocated:  158 kb [~ 0%]  <~1.50 kBlocks\r\nblocksize: 106  allocated: 79.5 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 107  allocated:  161 kb [~ 0%]  <~1.50 kBlocks\r\nblocksize: 108  allocated:  189 kb [~ 0%]  <~1.75 kBlocks\r\nblocksize: 110  allocated:  110 kb [~ 0%]  <~1.00 kBlocks\r\nblocksize: 111  allocated: 83.3 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 112  allocated: 56.0 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 113  allocated: 84.8 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 115  allocated:  173 kb [~ 0%]  <~1.50 kBlocks\r\nblocksize: 116  allocated:  290 kb [~ 0%]  <~2.50 kBlocks\r\nblocksize: 117  allocated:  263 kb [~ 0%]  <~2.25 kBlocks\r\nblocksize: 118  allocated: 88.5 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 120  allocated: 90.0 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 121  allocated:  182 kb [~ 0%]  <~1.50 kBlocks\r\nblocksize: 122  allocated:  275 kb [~ 0%]  <~2.25 kBlocks\r\nblocksize: 123  allocated:  246 kb [~ 0%]  <~2.00 kBlocks\r\nblocksize: 125  allocated: 93.8 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 126  allocated: 63.0 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 127  allocated: 63.5 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 128  allocated: 64.0 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 130  allocated: 65.0 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 131  allocated: 32.8 kb [~ 0%]  <~  256 Blocks\r\nblocksize: 132  allocated: 99.0 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 133  allocated: 99.8 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 135  allocated:  169 kb [~ 0%]  <~1.25 kBlocks\r\nblocksize: 136  allocated:  170 kb [~ 0%]  <~1.25 kBlocks\r\nblocksize: 137  allocated:  103 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 138  allocated: 69.0 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 140  allocated:  140 kb [~ 0%]  <~1.00 kBlocks\r\nblocksize: 141  allocated: 70.5 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 142  allocated:  107 kb [~ 0%]  <~  768 Blocks\r\nblocksize: 143  allocated: 71.5 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 145  allocated:  145 kb [~ 0%]  <~1.00 kBlocks\r\nblocksize: 146  allocated:  256 kb [~ 0%]  <~1.75 kBlocks\r\nblocksize: 147  allocated:  257 kb [~ 0%]  <~1.75 kBlocks\r\nblocksize: 148  allocated:  148 kb [~ 0%]  <~1.00 kBlocks\r\nblocksize: 150  allocated: 37.5 kb [~ 0%]  <~  256 Blocks\r\nblocksize: 151  allocated: 75.5 kb [~ 0%]  <~  512 Blocks\r\nblocksize: 152  allocated:  152 kb [~ 0%]  <~1.00 \r\nsum of above:  511 Mb\r\noverall alloc: 511 Mb\r\nsum of above:  0 b\r\noverall alloc: 0 b\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/epruesse/SINA/issues/comments/465426537","html_url":"https://github.com/epruesse/SINA/issues/53#issuecomment-465426537","issue_url":"https://api.github.com/repos/epruesse/SINA/issues/53","id":465426537,"node_id":"MDEyOklzc3VlQ29tbWVudDQ2NTQyNjUzNw==","user":{"login":"debjitde01","id":28703663,"node_id":"MDQ6VXNlcjI4NzAzNjYz","avatar_url":"https://avatars3.githubusercontent.com/u/28703663?v=4","gravatar_id":"","url":"https://api.github.com/users/debjitde01","html_url":"https://github.com/debjitde01","followers_url":"https://api.github.com/users/debjitde01/followers","following_url":"https://api.github.com/users/debjitde01/following{/other_user}","gists_url":"https://api.github.com/users/debjitde01/gists{/gist_id}","starred_url":"https://api.github.com/users/debjitde01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/debjitde01/subscriptions","organizations_url":"https://api.github.com/users/debjitde01/orgs","repos_url":"https://api.github.com/users/debjitde01/repos","events_url":"https://api.github.com/users/debjitde01/events{/privacy}","received_events_url":"https://api.github.com/users/debjitde01/received_events","type":"User","site_admin":false},"created_at":"2019-02-20T05:09:33Z","updated_at":"2019-02-20T05:09:33Z","author_association":"NONE","body":"Now i am trying with the recent version (1.5.0.) in conda and running with your given code, but i am getting an error (6th line from the first line of the script and the 3rd last line). Kindly help me to resolve this.\r\n\r\n(ddocent_env) pkd@pkd-HP-406-G1-MT:~/Downloads/sina-1.5.0-linux$ sina -i amplicons_seeds.fasta --db SILVA_132_SSURef_NR99_13_12_17_opt.arb -o sina_out.fasta --outtype fasta --search --meta-fmt csv --lca-fields tax_slv --fs-engine internal --num-pts 8 -v\r\n[2019-02-19 14:36:00.523] [log] [info] Loglevel set to info\r\n14:36:00 [SINA] This is SINA 1.5.0.\r\n14:36:00 [libARBDB] ARB: no FastLoad File 'SILVA_132_SSURef_NR99_13_12_17_opt.ARM' found => loading entire DB\r\n14:36:08 [ARB I/O] Loading names map... (for \"SILVA_132_SSURef_NR99_13_12_17_opt.arb\")\r\n\r\n0%   10   20   30   40   50   60   70   80   90   100%\r\n|----|----|----|----|----|----|----|----|----|----|\r\n***************************************************\r\n14:36:09 [Search (internal)] Index contains 695171 sequences (32088136 refs)\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:archaea\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1450/48550\r\n14:36:09 [alignment_stats] average weight = 4.87686\r\n14:36:09 [alignment_stats] minimum weight = 2.13805\r\n14:36:09 [alignment_stats] maximum weight = 7.29296\r\n14:36:09 [alignment_stats] ntaxa = 25025\r\n14:36:09 [alignment_stats] base frequencies: na=0.243357 nu=0.320127 nc=0.238212 ng=0.198304\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0212039 transversions=0.00822385\r\n14:36:09 [alignment_stats] first/last weighted column=1005/43115\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:bacteria\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1532/48468\r\n14:36:09 [alignment_stats] average weight = 5.2707\r\n14:36:09 [alignment_stats] minimum weight = 2.03587\r\n14:36:09 [alignment_stats] maximum weight = 7.67329\r\n14:36:09 [alignment_stats] ntaxa = 592559\r\n14:36:09 [alignment_stats] base frequencies: na=0.252611 nu=0.31454 nc=0.229764 ng=0.203085\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0167975 transversions=0.00775564\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43241\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:eukarya\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1836/48164\r\n14:36:09 [alignment_stats] average weight = 4.74158\r\n14:36:09 [alignment_stats] minimum weight = 2.09547\r\n14:36:09 [alignment_stats] maximum weight = 6.74351\r\n14:36:09 [alignment_stats] ntaxa = 77585\r\n14:36:09 [alignment_stats] base frequencies: na=0.257375 nu=0.268129 nc=0.211923 ng=0.262573\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0292276 transversions=0.0148656\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43273\r\n14:36:09 [SINA] Launching PT server no 1\r\n14:36:09 [SINA] Launching PT server no 4\r\n14:36:09 [SINA] Launching PT server no 6\r\n14:36:09 [SINA] Launching PT server no 7\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:archaea\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1450/48550\r\n14:36:09 [alignment_stats] average weight = 4.87686\r\n14:36:09 [alignment_stats] minimum weight = 2.13805\r\n14:36:09 [alignment_stats] maximum weight = 7.29296\r\n14:36:09 [alignment_stats] ntaxa = 25025\r\n14:36:09 [alignment_stats] base frequencies: na=0.243357 nu=0.320127 nc=0.238212 ng=0.198304\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0212039 transversions=0.00822385\r\n14:36:09 [alignment_stats] first/last weighted column=1005/43115\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:bacteria\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1532/48468\r\n14:36:09 [alignment_stats] average weight = 5.2707\r\n14:36:09 [alignment_stats] minimum weight = 2.03587\r\n14:36:09 [alignment_stats] maximum weight = 7.67329\r\n14:36:09 [alignment_stats] ntaxa = 592559\r\n14:36:09 [alignment_stats] base frequencies: na=0.252611 nu=0.31454 nc=0.229764 ng=0.203085\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0167975 transversions=0.00775564\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43241\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:eukarya\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1836/48164\r\n14:36:09 [alignment_stats] average weight = 4.74158\r\n14:36:09 [alignment_stats] minimum weight = 2.09547\r\n14:36:09 [alignment_stats] maximum weight = 6.74351\r\n14:36:09 [alignment_stats] ntaxa = 77585\r\n14:36:09 [alignment_stats] base frequencies: na=0.257375 nu=0.268129 nc=0.211923 ng=0.262573\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0292276 transversions=0.0148656\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43273\r\n14:36:09 [SINA] Launching PT server no 2\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:archaea\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1450/48550\r\n14:36:09 [alignment_stats] average weight = 4.87686\r\n14:36:09 [alignment_stats] minimum weight = 2.13805\r\n14:36:09 [alignment_stats] maximum weight = 7.29296\r\n14:36:09 [alignment_stats] ntaxa = 25025\r\n14:36:09 [alignment_stats] base frequencies: na=0.243357 nu=0.320127 nc=0.238212 ng=0.198304\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0212039 transversions=0.00822385\r\n14:36:09 [alignment_stats] first/last weighted column=1005/43115\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:bacteria\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1532/48468\r\n14:36:09 [alignment_stats] average weight = 5.2707\r\n14:36:09 [alignment_stats] minimum weight = 2.03587\r\n14:36:09 [alignment_stats] maximum weight = 7.67329\r\n14:36:09 [alignment_stats] ntaxa = 592559\r\n14:36:09 [alignment_stats] base frequencies: na=0.252611 nu=0.31454 nc=0.229764 ng=0.203085\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0167975 transversions=0.00775564\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43241\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:eukarya\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1836/48164\r\n14:36:09 [alignment_stats] average weight = 4.74158\r\n14:36:09 [alignment_stats] minimum weight = 2.09547\r\n14:36:09 [alignment_stats] maximum weight = 6.74351\r\n14:36:09 [alignment_stats] ntaxa = 77585\r\n14:36:09 [alignment_stats] base frequencies: na=0.257375 nu=0.268129 nc=0.211923 ng=0.262573\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0292276 transversions=0.0148656\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43273\r\n14:36:09 [SINA] Launching PT server no 3\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:archaea\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1450/48550\r\n14:36:09 [alignment_stats] average weight = 4.87686\r\n14:36:09 [alignment_stats] minimum weight = 2.13805\r\n14:36:09 [alignment_stats] maximum weight = 7.29296\r\n14:36:09 [alignment_stats] ntaxa = 25025\r\n14:36:09 [alignment_stats] base frequencies: na=0.243357 nu=0.320127 nc=0.238212 ng=0.198304\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0212039 transversions=0.00822385\r\n14:36:09 [alignment_stats] first/last weighted column=1005/43115\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:bacteria\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1532/48468\r\n14:36:09 [alignment_stats] average weight = 5.2707\r\n14:36:09 [alignment_stats] minimum weight = 2.03587\r\n14:36:09 [alignment_stats] maximum weight = 7.67329\r\n14:36:09 [alignment_stats] ntaxa = 592559\r\n14:36:09 [alignment_stats] base frequencies: na=0.252611 nu=0.31454 nc=0.229764 ng=0.203085\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0167975 transversions=0.00775564\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43241\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:eukarya\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1836/48164\r\n14:36:09 [alignment_stats] average weight = 4.74158\r\n14:36:09 [alignment_stats] minimum weight = 2.09547\r\n14:36:09 [alignment_stats] maximum weight = 6.74351\r\n14:36:09 [alignment_stats] ntaxa = 77585\r\n14:36:09 [alignment_stats] base frequencies: na=0.257375 nu=0.268129 nc=0.211923 ng=0.262573\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0292276 transversions=0.0148656\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43273\r\n14:36:09 [SINA] Launching PT server no 5\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:archaea\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1450/48550\r\n14:36:09 [alignment_stats] average weight = 4.87686\r\n14:36:09 [alignment_stats] minimum weight = 2.13805\r\n14:36:09 [alignment_stats] maximum weight = 7.29296\r\n14:36:09 [alignment_stats] ntaxa = 25025\r\n14:36:09 [alignment_stats] base frequencies: na=0.243357 nu=0.320127 nc=0.238212 ng=0.198304\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0212039 transversions=0.00822385\r\n14:36:09 [alignment_stats] first/last weighted column=1005/43115\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:bacteria\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1532/48468\r\n14:36:09 [alignment_stats] average weight = 5.2707\r\n14:36:09 [alignment_stats] minimum weight = 2.03587\r\n14:36:09 [alignment_stats] maximum weight = 7.67329\r\n14:36:09 [alignment_stats] ntaxa = 592559\r\n14:36:09 [alignment_stats] base frequencies: na=0.252611 nu=0.31454 nc=0.229764 ng=0.203085\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0167975 transversions=0.00775564\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43241\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:eukarya\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1836/48164\r\n14:36:09 [alignment_stats] average weight = 4.74158\r\n14:36:09 [alignment_stats] minimum weight = 2.09547\r\n14:36:09 [alignment_stats] maximum weight = 6.74351\r\n14:36:09 [alignment_stats] ntaxa = 77585\r\n14:36:09 [alignment_stats] base frequencies: na=0.257375 nu=0.268129 nc=0.211923 ng=0.262573\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0292276 transversions=0.0148656\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43273\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:archaea\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1450/48550\r\n14:36:09 [alignment_stats] average weight = 4.87686\r\n14:36:09 [alignment_stats] minimum weight = 2.13805\r\n14:36:09 [alignment_stats] maximum weight = 7.29296\r\n14:36:09 [alignment_stats] ntaxa = 25025\r\n14:36:09 [alignment_stats] base frequencies: na=0.243357 nu=0.320127 nc=0.238212 ng=0.198304\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0212039 transversions=0.00822385\r\n14:36:09 [alignment_stats] first/last weighted column=1005/43115\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:bacteria\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1532/48468\r\n14:36:09 [alignment_stats] average weight = 5.2707\r\n14:36:09 [alignment_stats] minimum weight = 2.03587\r\n14:36:09 [alignment_stats] maximum weight = 7.67329\r\n14:36:09 [alignment_stats] ntaxa = 592559\r\n14:36:09 [alignment_stats] base frequencies: na=0.252611 nu=0.31454 nc=0.229764 ng=0.203085\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0167975 transversions=0.00775564\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43241\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:eukarya\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1836/48164\r\n14:36:09 [alignment_stats] average weight = 4.74158\r\n14:36:09 [alignment_stats] minimum weight = 2.09547\r\n14:36:09 [alignment_stats] maximum weight = 6.74351\r\n14:36:09 [alignment_stats] ntaxa = 77585\r\n14:36:09 [alignment_stats] base frequencies: na=0.257375 nu=0.268129 nc=0.211923 ng=0.262573\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0292276 transversions=0.0148656\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43273\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:archaea\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1450/48550\r\n14:36:09 [alignment_stats] average weight = 4.87686\r\n14:36:09 [alignment_stats] minimum weight = 2.13805\r\n14:36:09 [alignment_stats] maximum weight = 7.29296\r\n14:36:09 [alignment_stats] ntaxa = 25025\r\n14:36:09 [alignment_stats] base frequencies: na=0.243357 nu=0.320127 nc=0.238212 ng=0.198304\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0212039 transversions=0.00822385\r\n14:36:09 [alignment_stats] first/last weighted column=1005/43115\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:bacteria\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1532/48468\r\n14:36:09 [alignment_stats] average weight = 5.2707\r\n14:36:09 [alignment_stats] minimum weight = 2.03587\r\n14:36:09 [alignment_stats] maximum weight = 7.67329\r\n14:36:09 [alignment_stats] ntaxa = 592559\r\n14:36:09 [alignment_stats] base frequencies: na=0.252611 nu=0.31454 nc=0.229764 ng=0.203085\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0167975 transversions=0.00775564\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43241\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:eukarya\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1836/48164\r\n14:36:09 [alignment_stats] average weight = 4.74158\r\n14:36:09 [alignment_stats] minimum weight = 2.09547\r\n14:36:09 [alignment_stats] maximum weight = 6.74351\r\n14:36:09 [alignment_stats] ntaxa = 77585\r\n14:36:09 [alignment_stats] base frequencies: na=0.257375 nu=0.268129 nc=0.211923 ng=0.262573\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0292276 transversions=0.0148656\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43273\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:archaea\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1450/48550\r\n14:36:09 [alignment_stats] average weight = 4.87686\r\n14:36:09 [alignment_stats] minimum weight = 2.13805\r\n14:36:09 [alignment_stats] maximum weight = 7.29296\r\n14:36:09 [alignment_stats] ntaxa = 25025\r\n14:36:09 [alignment_stats] base frequencies: na=0.243357 nu=0.320127 nc=0.238212 ng=0.198304\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0212039 transversions=0.00822385\r\n14:36:09 [alignment_stats] first/last weighted column=1005/43115\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:bacteria\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1532/48468\r\n14:36:09 [alignment_stats] average weight = 5.2707\r\n14:36:09 [alignment_stats] minimum weight = 2.03587\r\n14:36:09 [alignment_stats] maximum weight = 7.67329\r\n14:36:09 [alignment_stats] ntaxa = 592559\r\n14:36:09 [alignment_stats] base frequencies: na=0.252611 nu=0.31454 nc=0.229764 ng=0.203085\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0167975 transversions=0.00775564\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43241\r\n14:36:09 [alignment_stats] alignment stats for subset ssuref:eukarya\r\n14:36:09 [alignment_stats] weighted/unweighted columns = 1836/48164\r\n14:36:09 [alignment_stats] average weight = 4.74158\r\n14:36:09 [alignment_stats] minimum weight = 2.09547\r\n14:36:09 [alignment_stats] maximum weight = 6.74351\r\n14:36:09 [alignment_stats] ntaxa = 77585\r\n14:36:09 [alignment_stats] base frequencies: na=0.257375 nu=0.268129 nc=0.211923 ng=0.262573\r\n14:36:09 [alignment_stats] mutation frequencies: any=0.0292276 transversions=0.0148656\r\n14:36:09 [alignment_stats] first/last weighted column=1006/43273\r\n14:36:09 [Search (ARB PT)] Using ARBHOME=\"/home/pkd/anaconda3/envs/ddocent_env/lib/arb\"\r\n14:36:09 [Search (ARB PT)] PT server index out of date for SILVA_132_SSURef_NR99_13_12_17_opt.arb. Rebuilding:\r\nARB: Loading 'SILVA_132_SSURef_NR99_13_12_17_opt.arb.index.arb'\r\nARB: no FastLoad File 'SILVA_132_SSURef_NR99_13_12_17_opt.arb.index.ARM' found => loading entire DB\r\nARB: Loading 'SILVA_132_SSURef_NR99_13_12_17_opt.arb.index.arb' done\r\n\r\nProgress: Remove unused database entries\r\n...................................................................... [  8.3%] left: 1m49s\r\n...................................................................... [ 16.7%] left: 1m39s\r\n...................................................................... [ 25.0%] left: 1m27s\r\n...................................................................... [ 33.3%] left: 1m18s\r\n...................................................................... [ 41.7%] left: 1m8s\r\n...................................................................... [ 50.0%] left: 58s\r\n...................................................................... [ 58.3%] left: 48s\r\n...................................................................... [ 66.7%] left: 39s\r\n...................................................................... [ 75.0%] left: 30s\r\n...................................................................... [ 83.3%] left: 20s\r\n...................................................................... [ 91.7%] left: 10s\r\n...................................................................... [100.0%] used: 1m57s\r\n[done]\r\nDatabase contains 695171 species\r\nProgress: Preparing sequence data\r\n...................................................................... [  8.3%] left: 1m38s\r\n...................................................................... [ 16.7%] left: 1m34s\r\n...................................................................... [ 25.0%] left: 1m24s\r\n...................................................................... 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[100.0%] used: 1m55s\r\n[done]\r\n\r\nAll species contain data in alignment 'ali_16s'.\r\n[ptserver '-build_clean' took 6m41s]\r\nsum of above:  0 b\r\noverall alloc: 0 b\r\nsum of above:  0 b\r\noverall alloc: 0 b\r\nARB: Loading 'SILVA_132_SSURef_NR99_13_12_17_opt.arb.index.arb'\r\nARB: Opening FastLoad File 'SILVA_132_SSURef_NR99_13_12_17_opt.arb.index.ARM' ...\r\nARB: Loading 'SILVA_132_SSURef_NR99_13_12_17_opt.arb.index.arb' done\r\n\r\nBuilding PT-Server for alignment 'ali_16s'...\r\nDatabase contains 695171 species\r\nProgress: Checking data\r\n...................................................................... [  8.3%] left: 1m16s\r\n...................................................................... [ 16.7%] left: 40s\r\n...................................................................... [ 25.0%] left: 27s\r\n...................................................................... 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[100.0%] used: 15s\r\n[done]\r\nFailed to write to '/home/pkd/anaconda3/envs/ddocent_env/lib/arb/lib/pts/ptserver.log'\r\nVisible memory: 11.7 Gb\r\nRestricting used memory (by internal default '90%') to 10.5 Gb\r\nNote: Setting envar ARB_MEMORY will override that restriction (percentage or absolute memsize)\r\nMemory available for build: 9.21 Gb\r\nEstimated memory usage for 1 pass: 6.02 Gb\r\nOverall bases:       964 Mbp\r\nMax. partition size: 964 Mbp (=100.0%)\r\nProgress: Build index in 1 passes\r\n{pass 1/1}............................................................ [  8.3%] left: 15m16s\r\n...................................................................... [ 16.7%] left: 15m36s\r\n...................................................................... [ 25.0%] left: 14m36s\r\n...................................................................... [ 33.3%] left: 13m10s\r\n...................................................................... [ 41.7%] left: 11m40s\r\n...................................................................... [ 50.0%] left: 10m6s\r\n...................................................................... [ 58.3%] left: 8m30s\r\n...................................................................... [ 66.7%] left: 6m53s\r\n...................................................................... [ 75.0%] left: 5m17s\r\n..........................................................Killed\r\n05:57:19 [FASTA I/O] read -1 sequences from -1 lines\r\n05:57:25 [SINA] Error during program execution: Failed to (re)build PT server index! (out of memory?)\r\n05:57:25 [ARB I/O] Closing ARB database '\"SILVA_132_SSURef_NR99_13_12_17_opt.arb\"' ...\r\n06:02:54 [Search (internal)] Timings for Kmer Search: never called\r\n"}}
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