Failing to load db index

[MPourjam]

Although the index for database is built and exists in the same directory with the database file, Sina throws the error of 'Failed to load "path/to/index" - rebuilding'

[epruesse]

Odd. Can you elaborate?

• where did you get the build from?
• what parameters and data did you use?

Some conditions under which this would occur

• The index got corrupted somehow, e.g. because the disk was full or your storage quota exceeded
• You changed the size of k between runs
• You updated the source database (should give a different message though)

[MPourjam]

I am using Sina in pipeline. It needs to get run through an iteration with the arguments below:
sina-1.7 --in {} --search --meta-fmt csv --threads {} --lca-fields tax_slv --turn --search-max-result 100 --db {the absolute path to SILVA ARB SSURef99 } --out {The path to output file} --search-min-sim 0.9 --lca-quorum 0.7 --search-no-fast > /dev/null

Even after removing the build and letting the Sina creates it and store it, it still throws the error : "[Search (internal)] argument index 14:23:42 [Search (internal)] Failed to load "/path/to/db/SILVA-RefNR/SILVA138_SSURefNR99_120620.sidx" - rebuilding"
The data files are regular FASTA files.

Thank you very much.

[ilnamkang]

I've experienced the same problem.

(1) I've downloaded "sina-1.7.2-linux.tar.gz" from this repository, decompressed it, and used the binary within "sina-1.7.2-linux/bin".

(2) My command was as below. I had used the same command for the previous run, except for input and output files.

sina -i input.fasta -r SILVA_138.1_SSURef_NR99_12_06_20_opt.arb -o output.fasta -o output.csv --turn --search --fs-full-len=1300 --lca-fields=tax_slv --show-conf --intype=fasta --preserve-order --fasta-write-dna --fasta-write-dots --csv-crlf --overhang=remove --lowercase=unaligned --insertion=forbid --pen-gapext=2 --calc-idty --fs-kmer-no-fast --search-iupac=pessimistic

(3) Free space in my disk is >20 TB, so I think that the index was not corrupted.

(4) I used the same source database and didn't changed the size of k.

Anyway, SINA worked fine after rebuilding the index, which required 15-20 min on my machine (Ubuntu 18.04).

Below, I attach the stdout of the run.
-----
19:21:54 [SINA] This is SINA 1.7.2.
Effective parameters:
add-relatives = 0
auto-filter-field =
auto-filter-threshold = 0.8
calc-idty = 1
colors = 0
csv-crlf = 1
csv-id = name
csv-sep =
db = "SILVA_138.1_SSURef_NR99_12_06_20_opt.arb"
debug-graph = 0
fasta-block = 0
fasta-idx = 0
fasta-write-dna = 1
fasta-write-dots = 1
filter =
fs-cover-gene = 0
fs-engine = internal
fs-full-len = 1300
fs-kmer-len = 10
fs-kmer-mm = 0
fs-kmer-no-fast = 1
fs-kmer-norel = 0
fs-leave-query-out = 0
fs-max = 40
fs-min = 40
fs-min-len = 150
fs-msc = 0.7
fs-msc-max = 2
fs-no-graph = 0
fs-oldmatch = 0
fs-req = 1
fs-req-full = 1
fs-req-gaps = 10
fs-weight = 1
gene-end = 0
gene-start = 0
in = "input.fasta"
insertion = forbid
intype = FASTA
lca-fields = tax_slv
lca-quorum = 0.7
line-length = 0
lowercase = unaligned
markaligned = 0
markcopied = 0
match-score = 2
max-in-flight = 160
meta-fmt = none
min-idty = 0
mismatch-score = -1
no-align = 0
num-pts = 80
out = "output.fasta" "output.csv"
overhang = remove
pen-gap = 5
pen-gapext = 2
prealigned = 0
preserve-order = 1
prot-level = 4
ptport = :/tmp/sina_pt_81559
realign = 0
search = 1
search-all = 0
search-copy-fields =
search-correction = none
search-cover = query
search-filter-lowercase = 0
search-ignore-super = 0
search-iupac = pessimistic
search-kmer-candidates = 1000
search-kmer-len = 10
search-kmer-mm = 0
search-kmer-norel = 0
search-max-result = 10
search-min-sim = 0.7
search-no-fast = 0
search-port = :/tmp/sina_pt2_81559
select-file =
select-skip = 0
select-step = 1
show-conf =
show-diff = 0
show-dist = 0
threads = 4294967295
turn = revcomp
use-subst-matrix = 0
write-used-rels = 0

Processing: 0 [00:00:04]
19:21:58 [Search (internal)] Failed to load "SILVA_138.1_SSURef_NR99_12_06_20_opt.sidx" - rebuilding
19:31:20 [famfinder] Using internal engine for reference search
Processing: 0 [00:09:26]██████████████████████████████████████████████████████████████████████████████████████| 1048576/1048576 [00:09:18 / 00:00:00]
19:31:20 [Search (internal)] Failed to load "SILVA_138.1_SSURef_NR99_12_06_20_opt.sidx" - rebuilding
19:39:58 [SINA] Aligner ready. Processing sequences
19:39:59 [SINA] Took 0.721s to align 24 sequences (33.2428 sequences/s)
19:39:59 [SINA] SINA finished.
19:39:59 [ARB I/O] Closing ARB database '"SILVA_138.1_SSURef_NR99_12_06_20_opt.arb"' ...
-----

[Lorcaserin]

Hello,

I have a similar issue which seems to be linked to the --search-no-fast & --fs-kmer-no-fast parameters.
I am trying to replicate online SILVA tool default parameters and when I use --search-no-fast or --fs-kmer-no-fast, my database (SSU Ref NR99) which worked with the parameter off, goes into rebuilding the index and after, I believe, yields a similar result (almost) to when the parameter is off (as I compared with the online SILVA tool's output) & needs to rebuild the index everytime one of those parameter is switched on.

Below is my command: (my input is a fasta file)
sina -i $query -o $output -r SILVA_138.1_SSURef_NR99.arb --outtype=csv --search --search-db SILVA_138.1_SSURef_NR99.arb --lca-quorum=0.8 --min-idty=0.9 --lca-fields tax_slv --fields align_quality_slv,lca_tax_slv --preserve-order --show-conf --search-no-fast

Find below the stdout of the run

---

08:23:14 [SINA] This is SINA 1.7.2.
Effective parameters:
add-relatives = 0
auto-filter-field =
auto-filter-threshold = 0.8
calc-idty = 0
colors = 0
csv-crlf = 0
csv-id = name
csv-sep =
db = "/Raw_data/SILVA_138.1_SSURef_NR99.arb"
debug-graph = 0
fasta-block = 0
fasta-idx = 0
fasta-write-dna = 0
fasta-write-dots = 0
fields = align_quality_slv,lca_tax_slv
filter =
fs-cover-gene = 0
fs-engine = internal
fs-full-len = 1400
fs-kmer-len = 10
fs-kmer-mm = 0
fs-kmer-no-fast = 0
fs-kmer-norel = 0
fs-leave-query-out = 0
fs-max = 40
fs-min = 40
fs-min-len = 150
fs-msc = 0.7
fs-msc-max = 2
fs-no-graph = 0
fs-oldmatch = 0
fs-req = 1
fs-req-full = 1
fs-req-gaps = 10
fs-weight = 1
gene-end = 0
gene-start = 0
in = "/Raw_data/input.fasta"
insertion = shift
intype = AUTO
lca-fields = tax_slv
lca-quorum = 0.8
line-length = 0
lowercase = none
markaligned = 0
markcopied = 0
match-score = 2
max-in-flight = 20
meta-fmt = none
min-idty = 0.9
mismatch-score = -1
no-align = 0
num-pts = 10
out = "/Results/result.csv"
outtype = CSV
overhang = attach
pen-gap = 5
pen-gapext = 2
prealigned = 0
preserve-order = 1
prot-level = 4
ptport = :/tmp/sina_pt_188530
realign = 0
search = 1
search-all = 0
search-copy-fields =
search-correction = none
search-cover = query
search-db = "/Raw_data/SILVA_138.1_SSURef_NR99.arb"
search-filter-lowercase = 0
search-ignore-super = 0
search-iupac = optimistic
search-kmer-candidates = 1000
search-kmer-len = 10
search-kmer-mm = 0
search-kmer-norel = 0
search-max-result = 10
search-min-sim = 0.7
search-no-fast = 1
search-port = :/tmp/sina_pt2_188530
select-file =
select-skip = 0
select-step = 1
show-conf =
show-diff = 0
show-dist = 0
threads = 4294967295
turn = none
use-subst-matrix = 0
write-used-rels = 0

08:23:20 [famfinder] Using internal engine for reference search
Processing: 0 [00:00:05]███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 510508/510508 [00:00:00 / 00:00:00]
08:23:20 [Search (internal)] Failed to load "/Raw_data/SILVA_138.1_SSURef_NR99.sidx" - rebuilding
08:29:10 [SINA] Aligner ready. Processing sequences
08:29:44 [SINA] Took 34.455s to align 1258 sequences (36.5108 sequences/s)
08:29:44 [SINA] SINA finished.
08:29:44 [ARB I/O] Closing ARB database '"/Raw_data/SILVA_138.1_SSURef_NR99.arb"' ...