PDF create #14
Comments
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Hi there, |
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It's about 5.0Gb each. Not processed. Category A has only 51 pair and I think our MP is really poor quality. But we have other data set. |
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Ok, thanks. Well I'll certainly try and fix it for the next release. |
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Thanks. I will look forward it. |
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Dear Richard,
I try to get pdf report but there is some error.
I pasted latex/10k.log below.
Every analysis was done without error.
The error is
!pdfTeX error: pdflatex (file /Volumes/won/wgs/mp/10k_nextclip/graphs/10k_pe_A.
pdf): PDF inclusion: required page does not exist <0>
Also I checked /Volumes/won/wgs/mp/10k_nextclip/graphs/10k_pe_A.pdf and I can't open it.
Because of /Volumes/won/wgs/mp/10k_nextclip/analysis/10k_A_pe.txt is empty.
In log file, it looks fine.
Plotting insert size lengths for category A kind pe
Input: /Volumes/won/wgs/mp/10k_nextclip/analysis/10k_A_pe.txt
Output: /Volumes/won/wgs/mp/10k_nextclip/graphs/10k_pe_A.pdf
So If I did command below
$ cp 10k_pe_B.pdf 10k_pe_A.pdf
$ /Users/wyim/bin/nextclip/scripts/nextclip_make_report.pl -libdir /Volumes/won/wgs/mp/10k_nextclip -libname 10k -reference 'consensus.fasta' -organism 'Ice plant' -log /Volumes/won/wgs/mp/10k_nextclip/logs/nextclip_analysis.log -nextclip /Volumes/won/wgs/mp/10k_nextclip/logs/nextclip.log
I've got another error at latex/10k.log
!pdfTeX error: pdflatex (file /Volumes/won/wgs/mp/10k_nextclip/graphs/10k_tande
m_A.pdf): PDF inclusion: required page does not exist <0>
==> Fatal error occurred, no output PDF file produced!
$ cp 10k_tandem_B.pdf 10k_tandem_A.pdf
$ /Users/wyim/bin/nextclip/scripts/nextclip_make_report.pl -libdir /Volumes/won/wgs/mp/10k_nextclip -libname 10k -reference 'consensus.fasta' -organism 'Ice plant' -log /Volumes/won/wgs/mp/10k_nextclip/logs/nextclip_analysis.log -nextclip /Volumes/won/wgs/mp/10k_nextclip/logs/nextclip.log
And I finally got the report PDF.
I think this is an issue from empty analysis file.
Won
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex 2014.5.25) 12 DEC 2014 10:00
entering extended mode
\write18 enabled.
file:line:error style messages enabled.
%&-line parsing enabled.
**/Volumes/won/wgs/mp/10k_nextclip/latex/10k.tex
(/Volumes/won/wgs/mp/10k_nextclip/latex/10k.tex
LaTeX2e <2014/05/01>
Babel <3.9k> and hyphenation patterns for 78 languages loaded.
(/usr/local/texlive/2014/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2014/texmf-dist/tex/latex/base/size11.clo
File: size11.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=\dimen102
) (/usr/local/texlive/2014/texmf-dist/tex/latex/graphics/graphicx.sty
Package: graphicx 2014/04/25 v1.0g Enhanced LaTeX Graphics (DPC,SPQR)
(/usr/local/texlive/2014/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/05/08 v1.15 key=value parser (DPC)
\KV@toks@=\toks14
) (/usr/local/texlive/2014/texmf-dist/tex/latex/graphics/graphics.sty
Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
(/usr/local/texlive/2014/texmf-dist/tex/latex/graphics/trig.sty
Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
) (/usr/local/texlive/2014/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: pdftex.def on input line 91.
(/usr/local/texlive/2014/texmf-dist/tex/latex/pdftex-def/pdftex.def
File: pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX
(/usr/local/texlive/2014/texmf-dist/tex/generic/oberdiek/infwarerr.sty
Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages (HO)
) (/usr/local/texlive/2014/texmf-dist/tex/generic/oberdiek/ltxcmds.sty
Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO)
)
\Gread@gobject=\count87
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\Gin@req@height=\dimen103
\Gin@req@width=\dimen104
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\Urlmuskip=\muskip10
Package: url 2013/09/16 ver 3.4 Verb mode for urls, etc.
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(/usr/local/texlive/2014/texmf-dist/tex/latex/caption/caption.sty
Package: caption 2013/05/02 v3.3-89 Customizing captions (AR)
(/usr/local/texlive/2014/texmf-dist/tex/latex/caption/caption3.sty
Package: caption3 2013/05/02 v1.6-88 caption3 kernel (AR)
Package caption3 Info: TeX engine: e-TeX on input line 57.
\captionmargin=\dimen105
\captionmargin@=\dimen106
\captionwidth=\dimen107
\caption@tempdima=\dimen108
\caption@indent=\dimen109
\caption@parindent=\dimen110
\caption@hangindent=\dimen111
)
\c@ContinuedFloat=\count88
)
\c@subfigure=\count89
\c@subtable=\count90
) (/usr/local/texlive/2014/texmf-dist/tex/latex/rotating/rotating.sty
Package: rotating 2009/03/28 v2.16a rotated objects in LaTeX
(/usr/local/texlive/2014/texmf-dist/tex/latex/base/ifthen.sty
Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)
)
\c@r@tfl@t=\count91
\rotFPtop=\skip43
\rotFPbot=\skip44
\rot@float@box=\box26
\rot@mess@toks=\toks15
) (/usr/local/texlive/2014/texmf-dist/tex/latex/graphics/color.sty
Package: color 2014/04/23 v1.1a Standard LaTeX Color (DPC)
(/usr/local/texlive/2014/texmf-dist/tex/latex/latexconfig/color.cfg
File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive
)
Package color Info: Driver file: pdftex.def on input line 137.
) (/usr/local/texlive/2014/texmf-dist/tex/latex/titlesec/titlesec.sty
Package: titlesec 2011/12/15 v2.10.0 Sectioning titles
\ttl@box=\box27
\beforetitleunit=\skip45
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\ttl@plus=\dimen112
\ttl@minus=\dimen113
\ttl@toksa=\toks16
\titlewidth=\dimen114
\titlewidthlast=\dimen115
\titlewidthfirst=\dimen116
) (/usr/local/texlive/2014/texmf-dist/tex/latex/geometry/geometry.sty
Package: geometry 2010/09/12 v5.6 Page Geometry
(/usr/local/texlive/2014/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 detected.
) (/usr/local/texlive/2014/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/local/texlive/2014/texmf-dist/tex/generic/ifxetex/ifxetex.sty
Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
)
\Gm@cnth=\count92
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\c@Gm@tempcnt=\count94
\Gm@bindingoffset=\dimen117
\Gm@wd@mp=\dimen118
\Gm@odd@mp=\dimen119
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\Gm@layoutwidth=\dimen121
\Gm@layoutheight=\dimen122
\Gm@layouthoffset=\dimen123
\Gm@layoutvoffset=\dimen124
\Gm@dimlist=\toks17
) (/Volumes/won/wgs/mp/10k_nextclip/latex/10k.aux)
\openout1 = `10k.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
(/usr/local/texlive/2014/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
\scratchcounter=\count95
\scratchdimen=\dimen125
\scratchbox=\box28
\nofMPsegments=\count96
\nofMParguments=\count97
\everyMPshowfont=\toks18
\MPscratchCnt=\count98
\MPscratchDim=\dimen126
\MPnumerator=\count99
\makeMPintoPDFobject=\count100
\everyMPtoPDFconversion=\toks19
) (/usr/local/texlive/2014/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
Package: pdftexcmds 2011/11/29 v0.20 Utility functions of pdfTeX for LuaTeX (HO
)
(/usr/local/texlive/2014/texmf-dist/tex/generic/oberdiek/ifluatex.sty
Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)
Package ifluatex Info: LuaTeX not detected.
)
Package pdftexcmds Info: LuaTeX not detected.
Package pdftexcmds Info: \pdf@primitive is available.
Package pdftexcmds Info: \pdf@ifprimitive is available.
Package pdftexcmds Info: \pdfdraftmode found.
) (/usr/local/texlive/2014/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
Package: epstopdf-base 2010/02/09 v2.5 Base part for package epstopdf
(/usr/local/texlive/2014/texmf-dist/tex/latex/oberdiek/grfext.sty
Package: grfext 2010/08/19 v1.1 Manage graphics extensions (HO)
(/usr/local/texlive/2014/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty
Package: kvdefinekeys 2011/04/07 v1.3 Define keys (HO)
)) (/usr/local/texlive/2014/texmf-dist/tex/latex/oberdiek/kvoptions.sty
Package: kvoptions 2011/06/30 v3.11 Key value format for package options (HO)
(/usr/local/texlive/2014/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)
(/usr/local/texlive/2014/texmf-dist/tex/generic/oberdiek/etexcmds.sty
Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO)
Package etexcmds Info: Could not find \expanded.
(etexcmds) That can mean that you are not using pdfTeX 1.50 or
(etexcmds) that some package has redefined \expanded.
(etexcmds) In the latter case, load this package earlier.
)))
Package grfext Info: Graphics extension search list:
(grfext) .png,.pdf,.jpg,.mps,.jpeg,.jbig2,.jb2,.PNG,.PDF,.JPG,.JPE
G,.JBIG2,.JB2,.eps \AppendGraphicsExtensions on input line 452.
(/usr/local/texlive/2014/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
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Package caption Info: Begin \AtBeginDocument code.
Package caption Info: rotating package is loaded.
Package caption Info: End \AtBeginDocument code.
geometry driver: auto-detecting
geometry detected driver: pdftex
geometry verbose mode - [ preamble ] result:
LaTeX Font Info: External font
cmex10' loaded for size (Font) <9> on input line 17. LaTeX Font Info: External fontcmex10' loaded for size(Font) <6> on input line 17.
LaTeX Font Info: External font `cmex10' loaded for size
(Font) <5> on input line 17.
LaTeX Font Info: Try loading font information for OML+cmss on input line 57.
LaTeX Font Info: No file OMLcmss.fd. on input line 57.
LaTeX Font Warning: Font shape
OML/cmss/m/n' undefined (Font) usingOML/cmm/m/it' instead(Font) for symbol `textless' on input line 57.
</Volumes/won/wgs/mp/10k_nextclip/graphs/10k_mp_A.pdf, id=1, 216.81pt x 144.54p
t>
File: /Volumes/won/wgs/mp/10k_nextclip/graphs/10k_mp_A.pdf Graphic file (type p
df)
<use /Volumes/won/wgs/mp/10k_nextclip/graphs/10k_mp_A.pdf>
Package pdftex.def Info: /Volumes/won/wgs/mp/10k_nextclip/graphs/10k_mp_A.pdf u
sed on input line 66.
(pdftex.def) Requested size: 145.96312pt x 97.31325pt.
LaTeX Font Info: External font
cmex10' loaded for size (Font) <10.95> on input line 68. LaTeX Font Info: External fontcmex10' loaded for size(Font) <8> on input line 68.
!pdfTeX error: pdflatex (file /Volumes/won/wgs/mp/10k_nextclip/graphs/10k_pe_A.
pdf): PDF inclusion: required page does not exist <0>
==> Fatal error occurred, no output PDF file produced!
The text was updated successfully, but these errors were encountered: