SINA not running. showing Gave up (Reason: ARB ERROR: Expected entry 'baseoff' is missing for species 'A6BReg23' and Error during program execution: Failed to (re)build PT server index! (out of memory?)
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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12:34:53 [Search (ARB PT)] PT server index out of date for SSURef_NR99_132_SILVA_13_12_17_opt.arb.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
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...................................................................... [ 58.3%] left: 51s
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...................................................................... [ 91.7%] left: 10s
...................................................................... [100.0%] used: 2m3s
[done]
Database contains 695171 species
Progress: Preparing sequence data
...................................................................... [ 8.3%] left: 1m38s
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...................................................................... [ 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
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[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...