Open wyim-pgl opened 9 years ago
richardmleggett
commented
9 years ago Hi there, Thanks for this. You're right, it's a bug and I will try and fix it. However, I'm a bit surprised that you had no tandem or pe alignments. Were you using a very small file? Or some sort of already processed file? Thanks, Richard
wyim-pgl
commented
9 years ago It's about 5.0Gb each. Not processed.
Category A has only 51 pair and I think our MP is really poor quality. Because of this, there are no tandem and pe aligment.
But we have other data set.
richardmleggett
commented
9 years ago Ok, thanks. Well I'll certainly try and fix it for the next release.
wyim-pgl
commented
9 years ago Thanks. I will look forward it.
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
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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!