epruesse
commented
4 years ago Hi @tia-das - I won't have time to do fixes for 1.4.0 - try using the 1.6.x please.
This looks to be some issue with your ARB database though. Try re-downloading the SILVA database you are using, perhaps it got corrupted somehow.
i am trying to run SINA. The code is as follows: (my_env) pkd@pkd-HP-406-G1-MT:~/Desktop/Gargi/sequencing/another/Sina$ ARB_MEMORY=69% sina -i amplicons_seeds_uc.fasta --db SSURef_NR99_132_SILVA_13_12_17_opt.arb -o sina_out.fasta \ --search --meta-fmt csv --lca-fields tax_slv \ --fs-engine internal --num-pts 8 -v
The output is: [2019-11-26 12:34:43.161] [log] [info] Loglevel set to info 12:34:43 [SINA] This is SINA 1.4.0. 12:34:43 [libARBDB] ARB: no FastLoad File 'SSURef_NR99_132_SILVA_13_12_17_opt.ARM' found => loading entire DB 12:34:52 [ARB I/O] Loading names map... (for "SSURef_NR99_132_SILVA_13_12_17_opt.arb")
0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|
12:34:53 [Search (ARB PT)] Using ARBHOME="/home/pkd/anaconda3/envs/my_env/lib/arb" 12:34:53 [Search (ARB PT)] PT server index out of date for SSURef_NR99_132_SILVA_13_12_17_opt.arb. Rebuilding: ARB: Loading 'SSURef_NR99_132_SILVA_13_12_17_opt.arb.index.arb' Warning: modification times of DB and fastload file differ (DB=1574751894 fastload=1574682344 diff=69550) ARB: modification times of DB and fastload file differ (too much) => loading entire DB ARB: Loading 'SSURef_NR99_132_SILVA_13_12_17_opt.arb.index.arb' done
Progress: Remove unused database entries ...................................................................... [ 8.3%] left: 2m0s ...................................................................... [ 16.7%] left: 1m44s ...................................................................... [ 25.0%] left: 1m30s ...................................................................... [ 33.3%] left: 1m22s ...................................................................... [ 41.7%] left: 1m11s ...................................................................... [ 50.0%] left: 1m1s ...................................................................... [ 58.3%] left: 51s ...................................................................... [ 66.7%] left: 41s ...................................................................... [ 75.0%] left: 31s ...................................................................... [ 83.3%] left: 21s ...................................................................... [ 91.7%] left: 10s ...................................................................... [100.0%] used: 2m3s [done] Database contains 695171 species Progress: Preparing sequence data ...................................................................... [ 8.3%] left: 1m38s ...................................................................... [ 16.7%] left: 1m29s ...................................................................... [ 25.0%] left: 1m18s ...................................................................... [ 33.3%] left: 1m10s ...................................................................... [ 41.7%] left: 7m17s ...................................................................... [ 50.0%] left: 6m4s ...................................................................... [ 58.3%] left: 4m26s ...................................................................Killed ARB: Loading 'SSURef_NR99_132_SILVA_13_12_17_opt.arb.index.arb' Warning: modification times of DB and fastload file differ (DB=1574751894 fastload=1574682344 diff=69550) ARB: modification times of DB and fastload file differ (too much) => loading entire DB ARB: Loading 'SSURef_NR99_132_SILVA_13_12_17_opt.arb.index.arb' done
Building PT-Server for alignment 'ali_16s'... Database contains 695171 species Progress: Checking data ...................................................................... [100.0%] used: 0s ...................................................................... [200.0%] left: 0s ...................................................................... [300.0%] left: 0s ...................................................................... [400.0%] left: 0s ...................................................................... [500.0%] left: 0s ...................................................................... [600.0%] left: 0s ...................................................................... [700.0%] left: 0s ...................................................................... [800.0%] left: 0s ...................................................................... [900.0%] left: 0s ...................................................................... [1000.0%] left: 0s ...................................................................... [1100.0%] left: 0s ...................................................................... [1200.0%] left: 0s [done] Gave up (Reason: ARB ERROR: Expected entry 'baseoff' is missing for species 'A6BReg23') Failed to write to '/home/pkd/anaconda3/envs/my_env/lib/arb/lib/pts/ptserver.log' Failed to run 'arb_message 'Gave up (Reason: ARB ERROR: Expected entry "baseoff" is missing for species "A6BReg23")' &' /home/pkd/anaconda3/envs/my_env/lib/arb/bin/arb_pt_server: Error: Gave up (Reason: ARB ERROR: Expected entry 'baseoff' is missing for species 'A6BReg23') sum of above: 0 b overall alloc: 0 b sum of above: 0 b overall alloc: 0 b 13:07:22 [FASTA I/O] read -1 sequences from -1 lines 13:07:22 [SINA] Error during program execution: Failed to (re)build PT server index! (out of memory?) 13:07:23 [ARB I/O] Closing ARB database '"SSURef_NR99_132_SILVA_13_12_17_opt.arb"'
Thus, Sina is not running successfully. Kindly help me...