This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Arch Linux) (preloaded format=pdflatex 2022.11.8) 21 NOV 2022 16:54 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **mtDNA.tex (./mtDNA.tex LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2022-04-10> (/usr/share/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/10/04 v1.4n Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/size10.clo File: size10.clo 2021/10/04 v1.4n Standard LaTeX file (size option) ) \c@part=\count185 \c@section=\count186 \c@subsection=\count187 \c@subsubsection=\count188 \c@paragraph=\count189 \c@subparagraph=\count190 \c@figure=\count191 \c@table=\count192 \abovecaptionskip=\skip47 \belowcaptionskip=\skip48 \bibindent=\dimen138 ) (/usr/lib/R/library/msa/tex/texshade.sty Package: texshade 2021/04/01 LaTeX TeXshade (v1.26) Package `texshade', Version 1.26 of 2021/04/01. (/usr/share/texmf-dist/tex/latex/graphics/color.sty Package: color 2021/12/07 v1.3c Standard LaTeX Color (DPC) (/usr/share/texmf-dist/tex/latex/graphics-cfg/color.cfg File: color.cfg 2016/01/02 v1.6 sample color configuration ) Package color Info: Driver file: dvips.def on input line 149. (/usr/share/texmf-dist/tex/latex/graphics-def/dvips.def File: dvips.def 2017/06/20 v3.1d Graphics/color driver for dvips ) (/usr/share/texmf-dist/tex/latex/graphics/dvipsnam.def File: dvipsnam.def 2016/06/17 v3.0m Driver-dependent file (DPC,SPQR) )) (/usr/share/texmf-dist/tex/latex/graphics/graphics.sty Package: graphics 2021/03/04 v1.4d Standard LaTeX Graphics (DPC,SPQR) (/usr/share/texmf-dist/tex/latex/graphics/trig.sty Package: trig 2021/08/11 v1.11 sin cos tan (DPC) ) (/usr/share/texmf-dist/tex/latex/graphics-cfg/graphics.cfg File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration ) Package graphics Info: Driver file: pdftex.def on input line 107. (/usr/share/texmf-dist/tex/latex/graphics-def/pdftex.def File: pdftex.def 2020/10/05 v1.2a Graphics/color driver for pdftex )) \structurefile=\read2 \featurefile=\write3 \alignfile=\read3 \sublogofile=\read4 \exp@rtfile=\write4 \exp@rt@chimerafile=\write5 (/usr/share/texmf-dist/tex/latex/amsfonts/amssymb.sty Package: amssymb 2013/01/14 v3.01 AMS font symbols (/usr/share/texmf-dist/tex/latex/amsfonts/amsfonts.sty Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support \@emptytoks=\toks16 \symAMSa=\mathgroup4 \symAMSb=\mathgroup5 LaTeX Font Info: Redeclaring math symbol \hbar on input line 98. LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold' (Font) U/euf/m/n --> U/euf/b/n on input line 106. )) \symalphahelix=\mathgroup6 \loopcount=\count193 \innerloopcount=\count194 \outerloopcount=\count195 \seq@count=\count196 \killseq@count=\count197 \seq@percent=\count198 \res@count=\count199 \seq@pointer=\count266 \pos@count=\count267 \res@perline=\count268 \end@count=\count269 \cons@count=\count270 \total@count=\count271 \temp@count=\count272 \triple@count=\count273 \temp@@count=\count274 \pos@sum=\count275 \box@width=\skip49 \name@width=\skip50 \box@depth=\skip51 \width@tmp=\skip52 \box@height=\skip53 \number@width=\skip54 \line@stretch=\skip55 \center@fill=\skip56 \arrow@width=\skip57 \arrow@height=\skip58 \rule@thick=\skip59 \arrow@thick=\skip60 \logo@height=\skip61 \equal@width=\skip62 \equal@tmp=\skip63 \equal@height=\skip64 \temp@@length=\skip65 \vspace@legend=\skip66 \hspace@legend=\skip67 \bar@length=\skip68 Package color Info: Redefining color LightGray on input line 1716. Package color Info: Redefining color LightLightGray on input line 1817. Package color Info: Redefining color LightLightLightGray on input line 1919. ) (/usr/share/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def File: l3backend-pdftex.def 2022-04-14 L3 backend support: PDF output (pdfTeX) \l__color_backend_stack_int=\count276 \l__pdf_internal_box=\box50 ) No file mtDNA.aux. \openout1 = `mtDNA.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 24. LaTeX Font Info: ... okay on input line 24. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 24. LaTeX Font Info: ... okay on input line 24. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 24. LaTeX Font Info: ... okay on input line 24. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 24. LaTeX Font Info: ... okay on input line 24. LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 24. LaTeX Font Info: ... okay on input line 24. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 24. LaTeX Font Info: ... okay on input line 24. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 24. LaTeX Font Info: ... okay on input line 24. (/usr/share/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] \scratchcounter=\count277 \scratchdimen=\dimen139 \scratchbox=\box51 \nofMPsegments=\count278 \nofMParguments=\count279 \everyMPshowfont=\toks17 \MPscratchCnt=\count280 \MPscratchDim=\dimen140 \MPnumerator=\count281 \makeMPintoPDFobject=\count282 \everyMPtoPDFconversion=\toks18 ) (/usr/share/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty Package: epstopdf-base 2020-01-24 v2.11 Base part for package epstopdf Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4 85. (/usr/share/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv e )) (/tmp/Rtmp9tSm8e/seq57d10064df.fasta: Runaway argument? ! Paragraph ended before \inf@@get was complete. \par l.25 ...hade}{/tmp/Rtmp9tSm8e/seq57d10064df.fasta} I suspect you've forgotten a `}', causing me to apply this control sequence to too much text. How can we recover? My plan is to forget the whole thing and hope for the best. ! Misplaced alignment tab character &. \msfline ->\par & & & & @ l.25 ...hade}{/tmp/Rtmp9tSm8e/seq57d10064df.fasta} I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is simple: Just type `I\&' now. But if some right brace up above has ended a previous alignment prematurely, you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Misplaced alignment tab character &. \msfline ->\par & & & & @ l.25 ...hade}{/tmp/Rtmp9tSm8e/seq57d10064df.fasta} I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is simple: Just type `I\&' now. But if some right brace up above has ended a previous alignment prematurely, you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Misplaced alignment tab character &. \msfline ->\par & & & & @ l.25 ...hade}{/tmp/Rtmp9tSm8e/seq57d10064df.fasta} I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is simple: Just type `I\&' now. But if some right brace up above has ended a previous alignment prematurely, you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Misplaced alignment tab character &. \msfline ->\par & & & & @ l.25 ...hade}{/tmp/Rtmp9tSm8e/seq57d10064df.fasta} I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is simple: Just type `I\&' now. But if some right brace up above has ended a previous alignment prematurely, you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. Runaway argument? ! Paragraph ended before \check@letter was complete. \par l.25 ...hade}{/tmp/Rtmp9tSm8e/seq57d10064df.fasta} I suspect you've forgotten a `}', causing me to apply this control sequence to too much text. How can we recover? My plan is to forget the whole thing and hope for the best. Runaway argument? ! Paragraph ended before \firstchar@get was complete. \par l.25 ...hade}{/tmp/Rtmp9tSm8e/seq57d10064df.fasta} I suspect you've forgotten a `}', causing me to apply this control sequence to too much text. How can we recover? My plan is to forget the whole thing and hope for the best. Runaway argument? ! Paragraph ended before \firstchar@get was complete. \par l.47 \end{texshade} I suspect you've forgotten a `}', causing me to apply this control sequence to too much text. How can we recover? My plan is to forget the whole thing and hope for the best. Runaway argument? ! Paragraph ended before \res@get was complete. \par l.47 \end{texshade} I suspect you've forgotten a `}', causing me to apply this control sequence to too much text. How can we recover? My plan is to forget the whole thing and hope for the best. ! Misplaced alignment tab character &. \seq@line ->\par & @ l.47 \end{texshade} I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is simple: Just type `I\&' now. But if some right brace up above has ended a previous alignment prematurely, you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. . . . . . [1 Non-PDF special ignored! papersize=794.96999pt,614.295pt {/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] ) LaTeX Font Info: Trying to load font information for U+msa on input line 47. (/usr/share/texmf-dist/tex/latex/amsfonts/umsa.fd File: umsa.fd 2013/01/14 v3.01 AMS symbols A ) LaTeX Font Info: Trying to load font information for U+msb on input line 47. (/usr/share/texmf-dist/tex/latex/amsfonts/umsb.fd File: umsb.fd 2013/01/14 v3.01 AMS symbols B ) [2] (./mtDNA.aux) ) Here is how much of TeX's memory you used: 8179 strings out of 478238 97095 string characters out of 5850456 1334999 words of memory out of 5000000 26433 multiletter control sequences out of 15000+600000 471599 words of font info for 39 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 541i,6n,65p,182b,4214s stack positions out of 5000i,500n,10000p,200000b,80000s Output written on mtDNA.pdf (2 pages, 86917 bytes). PDF statistics: 26 PDF objects out of 1000 (max. 8388607) 15 compressed objects within 1 object stream 0 named destinations out of 1000 (max. 500000) 1 words of extra memory for PDF output out of 10000 (max. 10000000)