<html>
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<body bgcolor="#FFFFFF" text="#000000">
<p>Hi,</p>
<p>I'm the one who made the make conda package. The last time I
checked, it was working well, except I got some segfaults when
trying to use openmpi... I still plan to work on this, but I don't
know when exactly. Any help is welcome of course.</p>
<p>For your Inline C code, your problem was supposed to be fixed,
which version of Maker are you trying to install, with which
version of Conda (and which OS)?</p>
<p>Anthony Bretaudeau<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">Le 17/02/2019 à 19:50, Lior Glick a
écrit :<br>
</div>
<blockquote type="cite"
cite="mid:CAFOVipPHWZ++FwVdBMDuMx_PTRT2Ep-MZc=iD13ezT1bgrMZwg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">That's good to know. Any plans on creating a stable
conda package in the future? It'd be a very nice feature,
especially since MAKER is not always straightforward to install.</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Feb 13, 2019 at 5:22
PM Carson Holt <<a href="mailto:carsonhh@gmail.com"
moz-do-not-send="true">carsonhh@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">The conda recipe was
produced by another group. I do not currently recommend
using it because I have seen a number of issues pop up on
the list based on people attempting to install MAKER via
conda. I know there is at least an issue with the conda
RepeatMasker install, and there may be others. The specific
failure you show is from Bio::DB::IndexedBase trying to
compile an Inline::C function. It may be that conda is
installing an older BioPerl where this issue still exists
—> <a
href="https://github.com/bioperl/bioperl-live/issues/215"
target="_blank" moz-do-not-send="true">https://github.com/bioperl/bioperl-live/issues/215</a>
<div><br>
<div>Or it may be that there is a new related issue (I’ve
seen a handful of other examples that seem to relate
back to Bio::DB::IndexedBase) —> <a
href="https://github.com/bioperl/bioperl-live/issues/305"
style="font-family:Helvetica,Arial" target="_blank"
moz-do-not-send="true">https://github.com/bioperl/bioperl-live/issues/305</a></div>
<div><br>
</div>
<div>Try installing MAKER without conda (make sure to
remove any components that are in conda first to avoid
conflicts).</div>
<div><br>
</div>
<div>—Carson</div>
<div>
<div><br>
</div>
<div><br>
<blockquote type="cite">
<div>On Feb 13, 2019, at 5:20 AM, SARIGOEL, FATIH
<<a href="mailto:fatih.sarigoel@durham.ac.uk"
target="_blank" moz-do-not-send="true">fatih.sarigoel@durham.ac.uk</a>>
wrote:</div>
<br
class="gmail-m_3632822340552807500Apple-interchange-newline">
<div>
<div dir="ltr">
<div
id="gmail-m_3632822340552807500divtagdefaultwrapper"
style="font-size:12pt;font-family:Calibri,Helvetica,sans-serif"
dir="ltr">
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Greetings,</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
I notice that you never mention conda
installation on your website, so I am
curious if the conda version is actually
supposed to be working fine or not; as for
me it didn't.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
I created a new conda environment and
installed Maker (tried this with both
installation options)</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
When I run the example files, I get this
error:</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><br
class="gmail-m_3632822340552807500noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor">"make:
*** [Makefile:330: IndexedBase_14e0.o]
Error 127</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor">A
problem was encountered while attempting
to compile and install your Inline<br
class="gmail-m_3632822340552807500noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor">C
code. The command that failed was:</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor">
"make > out.make 2>&1" with
error code 2"</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><br
class="gmail-m_3632822340552807500noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor">My
conda environment is here</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor">/fast_new/work/users/fsarigo_m/miniconda3</span><br
class="gmail-m_3632822340552807500noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor">I don't understand why the
program is trying to look here:</span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor">/home/conda</span><br
class="gmail-m_3632822340552807500noBgColor">
</span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor">which
does not exist</span></span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><br
class="gmail-m_3632822340552807500noBgColor">
</span></span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor">Also
begins with a "possible precedence
issue"</span></span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><br
class="gmail-m_3632822340552807500noBgColor">
</span></span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor">Thanks
for your help in advance!</span></span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor">Fatih</span></span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><br
class="gmail-m_3632822340552807500noBgColor">
</span></span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor">+++++</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><br
class="gmail-m_3632822340552807500noBgColor">
</span></span></div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"><span
class="gmail-m_3632822340552807500noBgColor"><span
class="gmail-m_3632822340552807500noBgColor">Here
is the full log until the end of the
contig:</span></span></div>
<br
class="gmail-m_3632822340552807500noBgColor
gmail-m_3632822340552807500gmail-Apple-interchange-newline">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
(MakerX) [fsarigo_m@med0223 MAKER]$ maker</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Possible precedence issue with control flow
operator at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm
line 845.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
STATUS: Parsing control files...</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
STATUS: Processing and indexing input FASTA
files...</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
STATUS: Setting up database for any GFF3
input...</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
A data structure will be created for you at:</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_datastore</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
To access files for individual sequences use
the datastore index:</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_master_datastore_index.log</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
STATUS: Now running MAKER...</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
examining contents of the fasta file and run
log</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
--Next Contig--</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Processing run.log file...</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
#---------------------------------------------------------------------</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Now starting the contig!!</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
SeqID: contig-dpp-500-500</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Length: 32156</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
#---------------------------------------------------------------------</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Running Mkbootstrap for IndexedBase_14e0 ()</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
chmod 644 "IndexedBase_14e0.bs"</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/perl"
-MExtUtils::Command::MM -e 'cp_nonempty' --
IndexedBase_14e0.bs
blib/arch/auto/Bio/DB/IndexedBase_14e0/IndexedBase_14e0.bs
644</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/perl"
"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/ExtUtils/xsubpp"
-typemap
"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/5.26.2/ExtUtils/typemap"
IndexedBase_14e0.xs >
IndexedBase_14e0.xsc</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
mv IndexedBase_14e0.xsc IndexedBase_14e0.c</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc
-c
-I"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin"
-D_REENTRANT -D_GNU_SOURCE
--sysroot=/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/x86_64-conda_cos6-linux-gnu/sysroot
-fwrapv -fno-strict-aliasing -pipe
-fstack-protector-strong -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2
-O2 -DVERSION=\"0.00\"
-DXS_VERSION=\"0.00\" -fPIC
--sysroot=/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/x86_64-conda_cos6-linux-gnu/sysroot
"-I/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/5.26.2/x86_64-linux-thread-multi/CORE"
IndexedBase_14e0.c</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
/bin/sh:
/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc:
No such file or directory</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
make: *** [Makefile:330: IndexedBase_14e0.o]
Error 127</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
A problem was encountered while attempting
to compile and install your Inline</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
C code. The command that failed was:</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
"make > out.make 2>&1" with
error code 2</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
The build directory was:</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
To debug the problem, cd to the build
directory, and inspect the output files.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Environment PATH =
'/fast/users/fsarigo_m/miniconda3/envs/MakerX/bin:/fast/users/fsarigo_m/miniconda3/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/fast/users/fsarigo_m/.local/bin:/fast/users/fsarigo_m/bin'</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm
line 275.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
--> rank=NA, hostname=med0223</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>...propagated
at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm
line 869.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
--> rank=NA, hostname=med0223</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm
line 38.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>Error::_throw_Error_Simple(HASH(0x564b40c78870))
called at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm
line 306</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>Error::subs::run_clauses(HASH(0x564b40688970),
"Running Mkbootstrap for IndexedBase_14e0
()\x{a}chmod 644 \"Indexe"..., undef,
ARRAY(0x564b40673ad0)) called at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm
line 426</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>Error::subs::try(CODE(0x564b406899b8),
HASH(0x564b40688970)) called at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/FastaSeq.pm
line 95</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>FastaSeq::seq(FastaSeq=HASH(0x564b4068a7f0))
called at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm
line 478</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>Process::MpiChunk::_go(Process::MpiChunk=HASH(0x564b40673c08),
"run", HASH(0x564b40673c80), 0, 0) called at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm
line 341</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>Process::MpiChunk::run(Process::MpiChunk=HASH(0x564b40673c08),
0) called at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm
line 357</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x564b40673c08),
0) called at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiTiers.pm
line 287</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x564b4053f9f0),
0) called at
/fast/users/fsarigo_m/miniconda3/envs/MakerX/bin/maker
line 683</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Running Mkbootstrap for IndexedBase_14e0 ()</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
chmod 644 "IndexedBase_14e0.bs"</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/perl"
-MExtUtils::Command::MM -e 'cp_nonempty' --
IndexedBase_14e0.bs
blib/arch/auto/Bio/DB/IndexedBase_14e0/IndexedBase_14e0.bs
644</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/perl"
"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/ExtUtils/xsubpp"
-typemap
"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/5.26.2/ExtUtils/typemap"
IndexedBase_14e0.xs >
IndexedBase_14e0.xsc</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
mv IndexedBase_14e0.xsc IndexedBase_14e0.c</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc
-c
-I"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin"
-D_REENTRANT -D_GNU_SOURCE
--sysroot=/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/x86_64-conda_cos6-linux-gnu/sysroot
-fwrapv -fno-strict-aliasing -pipe
-fstack-protector-strong -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2
-O2 -DVERSION=\"0.00\"
-DXS_VERSION=\"0.00\" -fPIC
--sysroot=/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/x86_64-conda_cos6-linux-gnu/sysroot
"-I/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/5.26.2/x86_64-linux-thread-multi/CORE"
IndexedBase_14e0.c</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
/bin/sh:
/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc:
No such file or directory</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
make: *** [Makefile:330: IndexedBase_14e0.o]
Error 127</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
A problem was encountered while attempting
to compile and install your Inline</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
C code. The command that failed was:</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
"make > out.make 2>&1" with
error code 2</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
The build directory was:</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
To debug the problem, cd to the build
directory, and inspect the output files.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
Environment PATH =
'/fast/users/fsarigo_m/miniconda3/envs/MakerX/bin:/fast/users/fsarigo_m/miniconda3/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/fast/users/fsarigo_m/.local/bin:/fast/users/fsarigo_m/bin'</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm
line 275.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
--> rank=NA, hostname=med0223</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<span class="gmail-m_3632822340552807500gmail-noBgColor" style="white-space:pre-wrap"></span>...propagated
at
/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm
line 869.</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
--> rank=NA, hostname=med0223</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
--> rank=NA, hostname=med0223</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
--> rank=NA, hostname=med0223</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
ERROR: Failed while examining contents of
the fasta file and run log</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
ERROR: Chunk failed at level:0, tier_type:0</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
FAILED CONTIG:contig-dpp-500-500</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
<br
class="gmail-m_3632822340552807500gmail-noBgColor">
</div>
<div
class="gmail-m_3632822340552807500gmail-noBgColor"
style="font-family:Arial,Helvetica,sans-serif;font-size:small">
examining contents of the fasta file and run
log</div>
<div
class="gmail-m_3632822340552807500noBgColor"><br
class="gmail-m_3632822340552807500noBgColor">
</div>
<br
class="gmail-m_3632822340552807500noBgColor">
<div><br
class="gmail-m_3632822340552807500webkit-block-placeholder">
</div>
</div>
</div>
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