Does Conda Maker actually work?

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Does Conda Maker actually work?

SARIGOEL, FATIH

Greetings,
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.
I created a new conda environment and installed Maker (tried this with both installation options)
When I run the example files, I get this error:

"make: *** [Makefile:330: IndexedBase_14e0.o] Error 127
A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2"

My conda environment is here
/fast_new/work/users/fsarigo_m/miniconda3
I don't understand why the program is trying to look here:
/home/conda
which does not exist

Also begins with a "possible precedence issue"

Thanks for your help in advance!
Fatih

+++++

Here is the full log until the end of the contig:

(MakerX) [fsarigo_m@med0223 MAKER]$ maker
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.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/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
"/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
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/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
/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
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127

A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2

The build directory was:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0

To debug the problem, cd to the build directory, and inspect the output files.

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'
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
--> rank=NA, hostname=med0223
...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
--> rank=NA, hostname=med0223
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 38.
Error::_throw_Error_Simple(HASH(0x564b40c78870)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 306
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
Error::subs::try(CODE(0x564b406899b8), HASH(0x564b40688970)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/FastaSeq.pm line 95
FastaSeq::seq(FastaSeq=HASH(0x564b4068a7f0)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm line 478
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
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
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
Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x564b4053f9f0), 0) called at /fast/users/fsarigo_m/miniconda3/envs/MakerX/bin/maker line 683
Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/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
"/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
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/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
/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
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127

A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2

The build directory was:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0

To debug the problem, cd to the build directory, and inspect the output files.

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'
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
--> rank=NA, hostname=med0223
...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
--> rank=NA, hostname=med0223
--> rank=NA, hostname=med0223
--> rank=NA, hostname=med0223
ERROR: Failed while examining contents of the fasta file and run log
ERROR: Chunk failed at level:0, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



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Re: Does Conda Maker actually work?

Carson Holt-2
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 —> https://github.com/bioperl/bioperl-live/issues/215

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) —> https://github.com/bioperl/bioperl-live/issues/305

Try installing MAKER without conda (make sure to remove any components that are in conda first to avoid conflicts).

—Carson


On Feb 13, 2019, at 5:20 AM, SARIGOEL, FATIH <[hidden email]> wrote:

Greetings,
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.
I created a new conda environment and installed Maker (tried this with both installation options)
When I run the example files, I get this error:

"make: *** [Makefile:330: IndexedBase_14e0.o] Error 127
A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2"

My conda environment is here
/fast_new/work/users/fsarigo_m/miniconda3
I don't understand why the program is trying to look here:
/home/conda
which does not exist

Also begins with a "possible precedence issue"

Thanks for your help in advance!
Fatih

+++++

Here is the full log until the end of the contig:

(MakerX) [fsarigo_m@med0223 MAKER]$ maker
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.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/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
"/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
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/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
/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
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127

A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2

The build directory was:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0

To debug the problem, cd to the build directory, and inspect the output files.

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'
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
--> rank=NA, hostname=med0223
...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
--> rank=NA, hostname=med0223
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 38.
Error::_throw_Error_Simple(HASH(0x564b40c78870)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 306
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
Error::subs::try(CODE(0x564b406899b8), HASH(0x564b40688970)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/FastaSeq.pm line 95
FastaSeq::seq(FastaSeq=HASH(0x564b4068a7f0)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm line 478
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
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
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
Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x564b4053f9f0), 0) called at /fast/users/fsarigo_m/miniconda3/envs/MakerX/bin/maker line 683
Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/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
"/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
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/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
/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
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127

A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2

The build directory was:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0

To debug the problem, cd to the build directory, and inspect the output files.

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'
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
--> rank=NA, hostname=med0223
...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
--> rank=NA, hostname=med0223
--> rank=NA, hostname=med0223
--> rank=NA, hostname=med0223
ERROR: Failed while examining contents of the fasta file and run log
ERROR: Chunk failed at level:0, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



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Re: Does Conda Maker actually work?

Lior Glick-2
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.

On Wed, Feb 13, 2019 at 5:22 PM Carson Holt <[hidden email]> wrote:
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 —> https://github.com/bioperl/bioperl-live/issues/215

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) —> https://github.com/bioperl/bioperl-live/issues/305

Try installing MAKER without conda (make sure to remove any components that are in conda first to avoid conflicts).

—Carson


On Feb 13, 2019, at 5:20 AM, SARIGOEL, FATIH <[hidden email]> wrote:

Greetings,
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.
I created a new conda environment and installed Maker (tried this with both installation options)
When I run the example files, I get this error:

"make: *** [Makefile:330: IndexedBase_14e0.o] Error 127
A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2"

My conda environment is here
/fast_new/work/users/fsarigo_m/miniconda3
I don't understand why the program is trying to look here:
/home/conda
which does not exist

Also begins with a "possible precedence issue"

Thanks for your help in advance!
Fatih

+++++

Here is the full log until the end of the contig:

(MakerX) [fsarigo_m@med0223 MAKER]$ maker
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.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/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
"/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
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/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
/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
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127

A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2

The build directory was:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0

To debug the problem, cd to the build directory, and inspect the output files.

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'
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
--> rank=NA, hostname=med0223
...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
--> rank=NA, hostname=med0223
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 38.
Error::_throw_Error_Simple(HASH(0x564b40c78870)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 306
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
Error::subs::try(CODE(0x564b406899b8), HASH(0x564b40688970)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/FastaSeq.pm line 95
FastaSeq::seq(FastaSeq=HASH(0x564b4068a7f0)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm line 478
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
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
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
Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x564b4053f9f0), 0) called at /fast/users/fsarigo_m/miniconda3/envs/MakerX/bin/maker line 683
Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/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
"/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
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/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
/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
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127

A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2

The build directory was:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0

To debug the problem, cd to the build directory, and inspect the output files.

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'
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
--> rank=NA, hostname=med0223
...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
--> rank=NA, hostname=med0223
--> rank=NA, hostname=med0223
--> rank=NA, hostname=med0223
ERROR: Failed while examining contents of the fasta file and run log
ERROR: Chunk failed at level:0, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



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Re: Does Conda Maker actually work?

Anthony Bretaudeau-2

Hi,

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.

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)?

Anthony Bretaudeau


Le 17/02/2019 à 19:50, Lior Glick a écrit :
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.

On Wed, Feb 13, 2019 at 5:22 PM Carson Holt <[hidden email]> wrote:
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 —> https://github.com/bioperl/bioperl-live/issues/215

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) —> https://github.com/bioperl/bioperl-live/issues/305

Try installing MAKER without conda (make sure to remove any components that are in conda first to avoid conflicts).

—Carson


On Feb 13, 2019, at 5:20 AM, SARIGOEL, FATIH <[hidden email]> wrote:

Greetings,
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.
I created a new conda environment and installed Maker (tried this with both installation options)
When I run the example files, I get this error:

"make: *** [Makefile:330: IndexedBase_14e0.o] Error 127
A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2"

My conda environment is here
/fast_new/work/users/fsarigo_m/miniconda3
I don't understand why the program is trying to look here:
/home/conda
which does not exist

Also begins with a "possible precedence issue"

Thanks for your help in advance!
Fatih

+++++

Here is the full log until the end of the contig:

(MakerX) [fsarigo_m@med0223 MAKER]$ maker
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.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/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
"/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
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/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
/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
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127

A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2

The build directory was:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0

To debug the problem, cd to the build directory, and inspect the output files.

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'
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
--> rank=NA, hostname=med0223
...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
--> rank=NA, hostname=med0223
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 38.
Error::_throw_Error_Simple(HASH(0x564b40c78870)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 306
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
Error::subs::try(CODE(0x564b406899b8), HASH(0x564b40688970)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/FastaSeq.pm line 95
FastaSeq::seq(FastaSeq=HASH(0x564b4068a7f0)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm line 478
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
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
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
Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x564b4053f9f0), 0) called at /fast/users/fsarigo_m/miniconda3/envs/MakerX/bin/maker line 683
Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/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
"/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
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/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
/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
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127

A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
  "make > out.make 2>&1" with error code 2

The build directory was:
/fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0

To debug the problem, cd to the build directory, and inspect the output files.

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'
 at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
--> rank=NA, hostname=med0223
...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
--> rank=NA, hostname=med0223
--> rank=NA, hostname=med0223
--> rank=NA, hostname=med0223
ERROR: Failed while examining contents of the fasta file and run log
ERROR: Chunk failed at level:0, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



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