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Greetings,</div>
<div class="gmail-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>
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I created a new conda environment and installed Maker (tried this with both installation options)</div>
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When I run the example files, I get this error:</div>
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<div class="gmail-noBgColor"><br class=" noBgColor">
</div>
<div class="gmail-noBgColor">"make: *** [Makefile:330: IndexedBase_14e0.o] Error 127</div>
<div class="gmail-noBgColor">A problem was encountered while attempting to compile and install your Inline<br class=" noBgColor">
</div>
<div class="gmail-noBgColor">C code. The command that failed was:</div>
<div class="gmail-noBgColor"> "make > out.make 2>&1" with error code 2"</div>
<div class="gmail-noBgColor"><br class=" noBgColor">
</div>
<div class="gmail-noBgColor">My conda environment is here</div>
<div class="gmail-noBgColor"><span class=" noBgColor">/fast_new/work/users/fsarigo_m/miniconda3</span><br class=" noBgColor">
</div>
<div class="gmail-noBgColor"><span class=" noBgColor">I don't understand why the program is trying to look here:</span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor">/home/conda</span><br class=" noBgColor">
</span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor">which does not exist</span></span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor"><br class=" noBgColor">
</span></span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor">Also begins with a "possible precedence issue"</span></span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor"><br class=" noBgColor">
</span></span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor">Thanks for your help in advance!</span></span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor">Fatih</span></span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor"><br class=" noBgColor">
</span></span></div>
<div class="gmail-noBgColor">+++++</div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor"><br class=" noBgColor">
</span></span></div>
<div class="gmail-noBgColor"><span class=" noBgColor"><span class=" noBgColor">Here is the full log until the end of the contig:</span></span></div>
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(MakerX) [fsarigo_m@med0223 MAKER]$ maker</div>
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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>
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STATUS: Parsing control files...</div>
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STATUS: Processing and indexing input FASTA files...</div>
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STATUS: Setting up database for any GFF3 input...</div>
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A data structure will be created for you at:</div>
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/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_datastore</div>
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<br class="gmail-noBgColor">
</div>
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To access files for individual sequences use the datastore index:</div>
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/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_master_datastore_index.log</div>
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<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
STATUS: Now running MAKER...</div>
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examining contents of the fasta file and run log</div>
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</div>
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</div>
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</div>
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--Next Contig--</div>
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<br class="gmail-noBgColor">
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Processing run.log file...</div>
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#---------------------------------------------------------------------</div>
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Now starting the contig!!</div>
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SeqID: contig-dpp-500-500</div>
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Length: 32156</div>
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#---------------------------------------------------------------------</div>
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Running Mkbootstrap for IndexedBase_14e0 ()</div>
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chmod 644 "IndexedBase_14e0.bs"</div>
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"/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>
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"/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>
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mv IndexedBase_14e0.xsc IndexedBase_14e0.c</div>
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/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-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>
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make: *** [Makefile:330: IndexedBase_14e0.o] Error 127</div>
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<br class="gmail-noBgColor">
</div>
<div class="gmail-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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
C code. The command that failed was:</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
"make > out.make 2>&1" with error code 2</div>
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<br class="gmail-noBgColor">
</div>
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The build directory was:</div>
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/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0</div>
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<br class="gmail-noBgColor">
</div>
<div class="gmail-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>
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<br class="gmail-noBgColor">
</div>
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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-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>
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--> rank=NA, hostname=med0223</div>
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<span class="gmail-noBgColor" style="white-space: pre;"></span>...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.</div>
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--> rank=NA, hostname=med0223</div>
<div class="gmail-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>
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<span class="gmail-noBgColor" style="white-space: pre;"></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>
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<span class="gmail-noBgColor" style="white-space: pre;"></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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<span class="gmail-noBgColor" style="white-space: pre;"></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>
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<span class="gmail-noBgColor" style="white-space: pre;"></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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<span class="gmail-noBgColor" style="white-space: pre;"></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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<span class="gmail-noBgColor" style="white-space: pre;"></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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<span class="gmail-noBgColor" style="white-space: pre;"></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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<span class="gmail-noBgColor" style="white-space: pre;"></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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
Running Mkbootstrap for IndexedBase_14e0 ()</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
chmod 644 "IndexedBase_14e0.bs"</div>
<div class="gmail-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-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>
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mv IndexedBase_14e0.xsc IndexedBase_14e0.c</div>
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/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-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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<br class="gmail-noBgColor">
</div>
<div class="gmail-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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
C code. The command that failed was:</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
"make > out.make 2>&1" with error code 2</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<br class="gmail-noBgColor">
</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
The build directory was:</div>
<div class="gmail-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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<br class="gmail-noBgColor">
</div>
<div class="gmail-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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<br class="gmail-noBgColor">
</div>
<div class="gmail-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-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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
--> rank=NA, hostname=med0223</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<span class="gmail-noBgColor" style="white-space: pre;"></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-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
--> rank=NA, hostname=med0223</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
--> rank=NA, hostname=med0223</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
--> rank=NA, hostname=med0223</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
ERROR: Failed while examining contents of the fasta file and run log</div>
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ERROR: Chunk failed at level:0, tier_type:0</div>
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FAILED CONTIG:contig-dpp-500-500</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
<br class="gmail-noBgColor">
</div>
<div class="gmail-noBgColor" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">
examining contents of the fasta file and run log</div>
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