On Tue, 26 Jan 2016, Rich Shepard wrote:

 The problem seems related to the bibtex style file: apacite.sty. From the
displayed error log:

(/usr/share/texmf-dist/tex/latex/fragments/subscript.sty)
(/usr/share/texmf-d
ist/tex/latex/apacite/apacite.sty
Package: apacite 2013/07/21 v6.03 APA citation
! Undefined control sequence.
l.1216           \st@rtbibchapter

The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., hobx'), type      ' and the correct
spelling (e.g.,         \hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

  I've attached the document log file. The problem I now have is that the
referenced line numbers (which I assume is to what l.1216 refers) does not
contain the string \st@rtbibchapter. That line in the .lyx file is part of a
table.

  I can forward the .lyx file if that helps, it's 123K while the error file
is 31K. All errors in the log file refer to the bibliography and all of the
line numbers for each error is in a table.

Totally confused,

Rich
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014 on Slackware 
(SlackBuilds.org)) (preloaded format=latex 2015.7.22)  26 JAN 2016 11:49
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**coda-biota.tex
(./coda-biota.tex
LaTeX2e <2014/05/01>
Babel <3.9k> and hyphenation patterns for 78 languages loaded.

(/usr/share/texmf-dist/tex/latex/elsarticle/elsarticle.cls
Document Class: elsarticle 2009/09/17, 1.2.0: Elsevier Ltd
\@bls=\dimen102
(/usr/share/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-dist/tex/latex/base/size10.clo
File: size10.clo 2007/10/19 v1.4h Standard LaTeX file (size option)
)
\c@part=\count79
\c@section=\count80
\c@subsection=\count81
\c@subsubsection=\count82
\c@paragraph=\count83
\c@subparagraph=\count84
\c@figure=\count85
\c@table=\count86
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen103
) (/usr/share/texmf-dist/tex/latex/graphics/graphicx.sty
Package: graphicx 2014/04/25 v1.0g Enhanced LaTeX Graphics (DPC,SPQR)
(/usr/share/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/05/08 v1.15 key=value parser (DPC)
\KV@toks@=\toks14
) (/usr/share/texmf-dist/tex/latex/graphics/graphics.sty
Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
(/usr/share/texmf-dist/tex/latex/graphics/trig.sty
Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
) (/usr/share/texmf-dist/tex/latex/latexconfig/graphics.cfg
File: graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live
)
Package graphics Info: Driver file: dvips.def on input line 91.
(/usr/share/texmf-dist/tex/latex/graphics/dvips.def
File: dvips.def 2014/04/23 v3.0j Driver-dependant file (DPC,SPQR)
))
\Gin@req@height=\dimen104
\Gin@req@width=\dimen105
) (/usr/share/texmf-dist/tex/latex/psnfss/pifont.sty
Package: pifont 2005/04/12 PSNFSS-v9.2a Pi font support (SPQR) 
LaTeX Font Info:    Try loading font information for U+pzd on input line 63.
(/usr/share/texmf-dist/tex/latex/psnfss/upzd.fd
File: upzd.fd 2001/06/04 font definitions for U/pzd.
)
LaTeX Font Info:    Try loading font information for U+psy on input line 64.
(/usr/share/texmf-dist/tex/latex/psnfss/upsy.fd
File: upsy.fd 2001/06/04 font definitions for U/psy.
))
\c@tnote=\count87
\c@fnote=\count88
\c@cnote=\count89
\c@ead=\count90
\c@author=\count91
\@eadauthor=\toks15
\c@affn=\count92
\absbox=\box26
\keybox=\box27
\Columnwidth=\dimen106
\space@left=\dimen107
\els@boxa=\box28
\els@boxb=\box29
\leftMargin=\dimen108
\@enLab=\toks16
\@sep=\skip43
\@@sep=\skip44
(./coda-biota.spl) (/usr/share/texmf-dist/tex/latex/natbib/natbib.sty
Package: natbib 2010/09/13 8.31b (PWD, AO)
\bibhang=\skip45
\bibsep=\skip46
LaTeX Info: Redefining \cite on input line 694.
\c@NAT@ctr=\count93
)
\splwrite=\write3
\openout3 = `coda-biota.spl'.

) (/usr/share/texmf-dist/tex/latex/base/fontenc.sty
Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
(/usr/share/texmf-dist/tex/latex/base/t1enc.def
File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
LaTeX Font Info:    Redeclaring font encoding T1 on input line 43.
)) (/usr/share/texmf-dist/tex/latex/base/inputenc.sty
Package: inputenc 2014/04/30 v1.2b Input encoding file
\inpenc@prehook=\toks17
\inpenc@posthook=\toks18
(/usr/share/texmf-dist/tex/latex/base/latin9.def
File: latin9.def 2014/04/30 v1.2b Input encoding file
)) (/usr/share/texmf-dist/tex/latex/geometry/geometry.sty
Package: geometry 2010/09/12 v5.6 Page Geometry
(/usr/share/texmf-dist/tex/generic/oberdiek/ifpdf.sty
Package: ifpdf 2011/01/30 v2.3 Provides the ifpdf switch (HO)
Package ifpdf Info: pdfTeX in PDF mode is not detected.
) (/usr/share/texmf-dist/tex/generic/oberdiek/ifvtex.sty
Package: ifvtex 2010/03/01 v1.5 Detect VTeX and its facilities (HO)
Package ifvtex Info: VTeX not detected.
) (/usr/share/texmf-dist/tex/generic/ifxetex/ifxetex.sty
Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
)
\Gm@cnth=\count94
\Gm@cntv=\count95
\c@Gm@tempcnt=\count96
\Gm@bindingoffset=\dimen109
\Gm@wd@mp=\dimen110
\Gm@odd@mp=\dimen111
\Gm@even@mp=\dimen112
\Gm@layoutwidth=\dimen113
\Gm@layoutheight=\dimen114
\Gm@layouthoffset=\dimen115
\Gm@layoutvoffset=\dimen116
\Gm@dimlist=\toks19
) (/usr/share/texmf-dist/tex/latex/fragments/subscript.sty) (/usr/share/texmf-d
ist/tex/latex/apacite/apacite.sty
Package: apacite 2013/07/21 v6.03 APA citation
! Undefined control sequence.
l.1216           \st@rtbibchapter
                                 
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Too many }'s.
l.1219     }
            %
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.

! Undefined control sequence.
l.1220   \bibliographytypesize
                               % e.g., to put the bibliography in \small type
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Undefined control sequence.
l.1221   \bibliographyprenote
                               % some explanatory note before the references
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Undefined control sequence.
<argument> APAC@metaprenote@\APAC@extra@b@citeb 
                                                
l.1222 ...ed{APAC@metaprenote@\APAC@extra@b@citeb}
                                                  %
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Undefined control sequence.
<argument> \labelsep =\biblabelsep 
                                   \parsep =\bibparsep \itemsep =\bibitemsep...
l.1229                 \itemindent=\bibindent}
                                              % changed to cope with 4th ed.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.


! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1229                 \itemindent=\bibindent}
                                              % changed to cope with 4th ed.
You're in trouble here.  Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.

! Undefined control sequence.
<argument> ...p =\biblabelsep \parsep =\bibparsep 
                                                  \itemsep =\bibitemsep \lef...
l.1229                 \itemindent=\bibindent}
                                              % changed to cope with 4th ed.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Undefined control sequence.
<argument> ...p =\bibparsep \itemsep =\bibitemsep 
                                                  \leftmargin =\bibleftmargi...
l.1229                 \itemindent=\bibindent}
                                              % changed to cope with 4th ed.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Undefined control sequence.
<argument> ...itemsep \leftmargin =\bibleftmargin 
                                                  \itemindent =\bibindent 
l.1229                 \itemindent=\bibindent}
                                              % changed to cope with 4th ed.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Undefined control sequence.
l.1233    \bt@beg@thb@hook
                          
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Undefined control sequence.
l.1234    \APACrestorebibitem
                             
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.

! Too many }'s.
l.1235 }
        
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.

\c@BibCnt=\count97
\bibleftmargin=\skip47
\bibindent=\skip48
\bibparsep=\skip49
\bibitemsep=\skip50
\biblabelsep=\skip51
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(/usr/share/texmf-dist/tex/generic/babel-english/english.ldf
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File: babel.def 2014/03/24 3.9k Babel common definitions
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)
\l@canadian = a dialect from \language\l@american 
\l@australian = a dialect from \language\l@british 
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No file coda-biota.aux.
\openout1 = `coda-biota.aux'.

LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 32.
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(/usr/share/texmf-dist/tex/latex/base/ts1cmr.fd
File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions
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(/usr/share/texmf-dist/tex/latex/cbfonts-fd/lgrcmr.fd
File: lgrcmr.fd 2013/09/01 v1.0 Greek European Computer Regular
)
LaTeX Font Info:    ... okay on input line 32.
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\c@maskedRefs=\count99
(/usr/share/texmf-dist/tex/latex/apacite/english.apc
File: english.apc 2013/07/21 v6.03 apacite language file
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)
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Package natbib Warning: Citation `Sanchez2013' on page i undefined on input lin
e 94.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.118 \item
            Aquatic life. The water must be suitable as a habitat for fish and
Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.118 \item A
             quatic life. The water must be suitable as a habitat for fish and
Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.118 \item A
             quatic life. The water must be suitable as a habitat for fish and
Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.118 \item A
             quatic life. The water must be suitable as a habitat for fish and
Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.121 \item P
             ropagation of wildlife. The water must be suitable for the prop...

Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.121 \item P
             ropagation of wildlife. The water must be suitable for the prop...

Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.121 \item P
             ropagation of wildlife. The water must be suitable for the prop...

Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.123 \item W
             aters of extraordinary ecological or {\ae}sthetic value. The un...

Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.123 \item W
             aters of extraordinary ecological or {\ae}sthetic value. The un...

Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.123 \item W
             aters of extraordinary ecological or {\ae}sthetic value. The un...

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