<p dir="ltr">Anybody else experienced this error? Any ideas?<br>
Thanks </p>
<div class="gmail_quote">Em 15/10/2015 12:28, "Carlos Morais" <<a href="mailto:morais@iq.usp.br">morais@iq.usp.br</a>> escreveu:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Thanks a lot for the update.<br><br></div>However, it is trying to compile Jellyfish on the go. I'm attaching the output. Relevant part:<br><br><span style="font-family:monospace,monospace">Trinity version: v2.0.6<br>...<br>-------------------------------------------<br>----------- Jellyfish --------------------<br>-- (building a k-mer catalog from reads) --<br>-------------------------------------------<br><br>Wednesday, October 14, 2015: 13:46:18 CMD: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223 --canonical both.fa<br>mkdir: cannot create directory ‘/usr/bin/.libs’: Permission denied<br>/usr/bin/jellyfish: line 202: cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3: No such file or directory<br>g++: error: sub_commands/jellyfish.o: No such file or directory<br>g++: error: sub_commands/count_main.o: No such file or directory<br>g++: error: sub_commands/info_main.o: No such file or directory<br>g++: error: sub_commands/dump_main.o: No such file or directory<br>g++: error: sub_commands/histo_main.o: No such file or directory<br>g++: error: sub_commands/stats_main.o: No such file or directory<br>g++: error: sub_commands/merge_main.o: No such file or directory<br>g++: error: sub_commands/bc_main.o: No such file or directory<br>g++: error: sub_commands/query_main.o: No such file or directory<br>g++: error: sub_commands/cite_main.o: No such file or directory<br>g++: error: sub_commands/mem_main.o: No such file or directory<br>g++: error: jellyfish/merge_files.o: No such file or directory<br>g++: error: ./.libs/<a href="http://libjellyfish-2.0.so" target="_blank">libjellyfish-2.0.so</a>: No such file or directorynError, cmd: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223 --canonical both.fa died with ret 256 at /usr/lib/trinityrnaseq/Trinity line 2115.<br><br>Trinity run failed. Must investigate error above.</span><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran <span dir="ltr"><<a href="mailto:kirannbishwa01@gmail.com" target="_blank">kirannbishwa01@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks for the update !</div><div class="gmail_extra"><div><div><br><div class="gmail_quote">On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth <span dir="ltr"><<a href="mailto:tbooth@ceh.ac.uk" target="_blank">tbooth@ceh.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi All,<br>
<br>
I've been doing a round of package updates on Bio-Linux 8 over the last<br>
week. We now have both Mothur and Mira updated to the latest versions:<br>
<br>
mira-assembler package is version 4.9.5<br>
mothur package is version 1.36.1<br>
<br>
Both will be updated by the package updater. If you experience any<br>
problems or regressions with these new packages please let me know.<br>
<br>
I'm also pleased to say that the Trinity RNA-Seq De novo assembler has<br>
been added to the package repository (<a href="http://trinityrnaseq.github.io/" rel="noreferrer" target="_blank">http://trinityrnaseq.github.io/</a>).<br>
Various modifications have been made to Trinity to make it integrate<br>
nicely with the other packages on the system, so if you have problems<br>
running it please let me know and I'll check if it is maybe something<br>
that got messed up in the packaging.<br>
<br>
trinityrnaseq package is version 2.0.6<br>
<br>
To get it: sudo apt-get install trinityrnaseq<br>
then just type: "Trinity" (with the capital T)<br>
<br>
The credit for all this goes mainly to Michael and Andreas from the<br>
Debian Med project who maintain these packages in Debian. I've been<br>
able to take what they made and backport it to Bio-Linux for you.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<br>
--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk" target="_blank">tbooth@ceh.ac.uk</a>><br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://environmentalomics.org/bio-linux" rel="noreferrer" target="_blank">http://environmentalomics.org/bio-linux</a><br>
<a href="tel:%2B44%201491%2069%202297" value="+441491692297" target="_blank">+44 1491 69 2297</a><br>
<br>
<br>
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