Error when querying a compiled database

[Nate Upham]

Hi all
When I do the following call to query a pre-built datbase for Other Mammalia ("mam")...

PHLAWD.MAC assemble configMam.txt

I get this output and error message:

"using sqlite
assembly
number of threads: 4
clade name: Chiroptera
search: (description LIKE '%CYTB%' OR description LIKE '%cytochrome%' OR description LIKE '%cyt-b%') AND NOT (description LIKE '%oxidase%' OR description LIKE '%COX%')
gene name: cytb
mad cutoff: 0.01
coverage: 0.2
identity: 0.2
removing existing files
search number 1
connected to /MamDB/mam.db
Found 0 taxon ids:
Segmentation fault: 11"

Is this a segmentation error, or did it just fail to find any sequences given my criteria?

Here's the contents of the configMam.txt file:

"clade = Chiroptera
db = /MamDB/mam.db
mad = 0.01
coverage = 0.2
identity = 0.2
numthreads = 4
knownfile = /fastas/CYTB.fas
gene = cytb

search = (description LIKE '%CYTB%' OR description LIKE '%cytochrome%' OR description LIKE '%cyt-b%') AND NOT (description LIKE '%oxidase%' OR description LIKE '%COX%')

feature:
searchliteral"

Anyone have ideas?
Many thanks
--nate

[Stephen Smith]

it looks to me that maybe the db location isn't quite right. is that
possible?

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[Nate Upham]

Ah, okay, hmmm… it started to run after I moved the db to the same directory as the config file, but then it still terminated early with the same error:

"using sqlite

assembly
number of threads: 4
clade name: Chiroptera
search: (description LIKE '%CYTB%' OR description LIKE '%cytochrome%' OR description LIKE '%cyt-b%') AND NOT (description LIKE '%oxidase%' OR description LIKE '%COX%')
gene name: cytb
mad cutoff: 0.01
coverage: 0.2
identity: 0.2
removing existing files
search number 1

connected to mam.db
Found 1 taxon ids:
9397
Will be using 9397
first: 0
splitting: 0
splitting: 0
splitting: 0
splitting: 0
thread: 0
thread: 1
thread: 2
thread: 3
joining: 0
Completed join with thread 0 status= 0
joining: 1
Completed join with thread 1 status= 0
joining: 2
Completed join with thread 2 status= 0
joining: 3
Completed join with thread 3 status= 0
blasted: 0

dups: 0

leftovers: 0
removing existing files
getting file names
getting file names
Segmentation fault: 11"

It made several files and directories, but all are empty...

Thanks

—nate

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[Stephen Smith]

maybe the knownfile = /fastas/CYTB.fas isn't quite right either? might
need to be knownfile = fastas/CYTB.fas

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[Nate Upham]

I had changed that one as well. Config file contents:

"clade = Chiroptera
db = mam.db

mad = 0.01
coverage = 0.2
identity = 0.2
numthreads = 4

knownfile = CYTB.fas

gene = cytb

search = (description LIKE '%CYTB%' OR description LIKE '%cytochrome%' OR description LIKE '%cyt-b%') AND NOT (description LIKE '%oxidase%' OR description LIKE '%COX%')

feature:

searchliteral”

Thanks for your help Stephen

[Stephen Smith]

hm, you can send along the bait file, but basically it isn't finding
anything and then just dying because of that

[Nate Upham]

The CYTB.fas bait file is attached... formatting seems normal enough

I'm confused about Chiroptera not yielding any cytb hits though...

What is the expectation based on the "Segmentation fault: 11"?

Thanks
--n

[blackrim]

hm, I only see the config file. can you resend the seq file please.
thanks!

[Nate Upham]

Fasta file for cytb:

>Bos_taurus

ATGACTAACATTCGAAAGTCCCACCCACTAATAAAAATTGTAAACAATGCATTCATCGACCTTCCAGCCC

CATCGAACATTTCATCATGATGGAATTTCGGTTCCCTCCTGGGAATCTGCCTAATCCTACAAATCCTCAC

AGGCCTATTCCTAGCAATACACTACACATCCGACACAACAACAGCATTCTCCTCTGTTACCCATATCTGC

CGAGACGTGAACTACGGCTGAATCATCCGATACATACACGCAAACGGAGCTTCAATGTTTTTTATCTGCT

TATATATGCACGTAGGACGAGGCTTATATTATGGGTCTTACACTTTTCTAGAAACATGAAATATCGGAGT

AATCCTTCTGCTCACAGTAATAGCCACAGCATTCATAGGATACGTCCTACCATGAGGACAAATATCATTC

TGAGGAGCAACAGTCATCACCAACCTCTTATCAGCAATCCCATACATCGGCACAAATTTAGTCGAATGAA

TCTGAGGCGGATTTTCAGTAGACAAAGCAACCCTTACCCGATTTTTCGCTTTCCACTTTATCCTTCCATT

TATCATCATAGCAATTGCCATAGTCCACCTACTATTCCTCCACGAAACAGGCTCCAACAATCCAACAGGA

ATCTCCTCAGACGTAGACAAAATCCCATTCCACCCCTACTATACCATTAAGGACATCTTAGGGGCCCTCT

TACTAATTCTAGCTCTAATACTACTAGTACTATTTGCGCCCAACCTCCTCGGAGACCCAGATAACTACAC

CCCAGCCAATCCACTCAACACACCTCCTCACATCAAACCCGAGTGGTACTTCCTATTTGCATATGCAATT

CTACGATCAATCCCCAATAAACTAGGAGGAGTCCTAGCCCTAGTCTTCTCCATCCTAATCCTTATTCTCA

TTCCCTTACTACACACATCCAAACAGCGAAGCATAATATTCCGACTGCTCAGCCAATGCCTGTTCTGAAT

TTTAGTAGCAGACCTACTAACACTCACATGAATTGGAGGACAACCAGTTGAACATCCATACATCATCATT

GGACAACTAGCATCTATCATATACTTTCTCCTCATCCTAGTGCTAATACCAACAGCCGGCACAGTTGAAA

ACAACCTACTAAAATGAAGA

>Canis_lupus_familiaris

ATGACCAACATTCGAAAAACCCACCCACTAGCCAAAATTGTTAATAACTCATTCATTGACCTCCCAGCGC

CGTCTAACATCTCTGCTTGATGGAACTTCGGATCCTTACTAGGAGTATGCTTGATTCTACAGATTCTAAC

AGGTTTATTCTTAGCTATGCACTATACATCGGACACAGCCACAGCTTTTTCATCAGTCACCCACATCTGC

CGAGACGTTAACTACGGCTGAATTATCCGCTATATGCACGCAAATGGCGCTTCCATATTCTTTATCTGCC

TATTCCTACATGTAGGACGAGGCCTATATTACGGATCCTATGTATTCATAGAAACATGAAACATTGGAAT

TGTACTATTATTCGCAACCATAGCCACAGCATTCATGGGCTATGTACTACCATGAGGACAAATATCATTT

TGAGGAGCAACTGTAATCACTAATCTTCTCTCTGCCATCCCTTATATCGGAACTGACTTAGTAGAATGGA

TCTGAGGCGGCTTCTCAGTGGACAAAGCAACCCTAACACGATTCTTTGCATTCCATTTCATCCTCCCTTT

CATCATCGCAGCTCTAGCAATAGTACACCTCCTATTTCTACACGAAACCGGATCCAACAACCCTTCAGGA

ATCACATCAGACTCAGACAAAATTCCATTTCACCCTTACTACACAATCAAGGATATCCTAGGAGCCTTAC

TCCTACTCCTAATCCTAATATCACTAGTTTTATTTTCACCTGACCTATTAGGAGACCCAGATAACTACAC

CCCTGCAAACCCCCTAAACACCCCTCCACATATTAAACCTGAGTGATATTTCCTATTCGCCTATGCTATC

CTACGATCCATTCCTAATAAATTAGGAGGTGTACTCGCCCTAGTATTCTCCATCCTAATCTTGGCATTCA

TTCCACTCCTCCACACATCTAAGCAACGCAGCATAATATTCCGGCCCCTTAGCCAATGCCTATTCTGACT

TTTAGTCGCCGATCTTCTCACTTTAACATGAATTGGAGGACAACCAGTTGAACACCCTTTCATCATTATC

GGACAAGTCGCTTCAATCTTATATTTCACCATCTTATTGATCCTAATACCAACAGTTAGCGTTATCGAAA

ACAACCTTCTAAAATGAAGA

>Macaca_mulatta

ATGATACCAATACGCAAATCCAACCCAATCATAAAAATAATTAATCGCTCCTTCATTGATTTACCCACCC

CACCCAACCTCTCCATGTGATGAAACTTTGGCTCACTTCTTGCAGCCTGCCTAATTTTACAAATCATCAC

AGGCCTACTCCTAGCAATACACTACTCACCAGACACCTCCTCCGCCTTCTCCTCAATCGCACATATCACC

CGAGATGTAAAGTACGGTTGAATCACTCGCTACCTCCACGCCAATGGTGCCTCTATACTCTTTATCTGCC

TTTTCCTACACATCGGTCGAGGCCTTTACTACGGCTCATATCTCCTCCTAGAAACCTGAAACATTGGCAT

TATACTCCTTCTTATAACCATAACAACAGCTTTCATGGGTTATGTTCTCCCATGAGGCCAAATGTCATTC

TGGGGGGCAACAGTAATCACAAACCTACTGTCAGCAATTCCGTACATTGGAACCAATCTAGTCCAATGAA

TCTGAGGAGGATACGCCATCGGCAGCCCCACTCTCACACGATTCTTCACCTTACACTTTATCCTACCCTT

CATTATCATCGCCCTCACAACTGTACACCTGCTATTCCTACACGAAACAGGATCAAACAACCCTTGCGGA

ATCTCCTCCGACTCGGACAAAATCGCCTTCCACCCCTACTACACAATCAAAGACATCCTAGGCCTAGTCC

TCCTTCTCTTTACCCTAGCAACACTAACACTACTCTCACCCAACCTCCTAAACGACCCAGACAACTACAT

CCCGGCCGACCCACTAAACACTCCCCCACACATCAAGCCAGAATGATACTTCCTATTTGCATACACAATC

CTACGATCCATCCCCAACAAACTGGGAGGCGTACTAGCACTCTTCTTATCAATCCTCATCCTAGCAGCCA

TCCCCATACTCCACAAATCCAAACAACAAAGTATAATATTCCGCCCACTCAGCCAATTCCTGTTCTGACT

CCTAATAACAATCCTACTAACCCTTACCTGAATTGGAAGCGAACCAGTAACTCAACCCCTTATCACTATC

GGCCAAGTAGCATCCATAATATACTTCATCACAATTCTAATCCTAATACCACTGGACTCCCTAATCGAAA

ACAACCTACTCAAATGATCT

[Stephen Smith]

Sorry for the delay
OK, I am thinking that maybe just a few things aren't installed. Do you
have the libsqlitewrapper installed? quicktree and muscle and mafft?
I replicated the problem at the same stage by missing these.
Take care