Installation problems

[francicco]

Hi,

I'm reinstalling cactus due to conflict in the environment. I recompiled the kyoto libraries. Now what I did was

git clone https://github.com/ComparativeGenomicsToolkit/cactus.git
cd cactus
cd submodules && ln -s /mnt/storage/scratch/tk19812/software/clapack/ clapack (recompiled) && cd ..
virtualenv cactus_env
source cactus_env/bin/activate
pip install biopython boto3 coveralls cython deap ete3 gffutils graphviz matplotlib networkx numpy PyPDF2 pysam pytest pytest-cov PyYAML scipy seaborn 
pip install --upgrade toil

here I got this error:

Collecting actualSonLib (from progressiveCactus==1.0)
  ERROR: Could not find a version that satisfies the requirement actualSonLib (from progressiveCactus==1.0) (from versions: none)
ERROR: No matching distribution found for actualSonLib (from progressiveCactus==1.0)

then I did:

git submodule update --init
make
Building dependency sonLib
Building dependency pinchesAndCacti
Building dependency matchingAndOrdering
Building dependency cPecan
Building dependency hdf5
Building dependency hal

During hal I get this error:

inc/halPhyloP.h:16:24: fatal error: tree_model.h: No such file or directory

How should I fix this? Thanks a lot F

[diekhans]

look carefully at the line: g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o kcutiltest kcutiltest.o -L. -L/home/tk19812/software/cactus/lib -L/usr/local/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/libfabric/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib/release:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mpi/mic/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2018-u3/debugger_2018/iga/lib:/sw/lang/intel-psxe-2018-u3/debugger_2018/libipt/intel64/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/libfabric/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib/release:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/debugger_2019/libipt/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/sw/lib/hdf5-1.10.6/lib:/sw/lang/gcc-9.1.0/lib64:/sw/lang/gcc-9.1.0/lib:/home/tk19812/software/lua-5.3.5/lib:/home/tk19812/software/lzo-2.10/include -Wl,--as-needed -lkyotocabinet -lz -lstdc++ -lrt -lpthread -lm -lc

I have no idea how -Wl,-rpath-link, argument is being generated by you.

[francicco]

I just know that I execute the make in cactus dir like this:

CPPFLAGS=-I/home/tk19812/software/lzo-2.10/include/ LDFLAGS=-Wl,-rpath-link,-L/home/tk19812/software/lzo-2.10/lib make

to link the include and lib dirs F

[francicco]

ok, I get that, that -Wl,-rpath-link, was my mistake. It's running now... F

[francicco]

I moved the already compiled sonLib, phast, clapack and hal in the new location and I executed make

this is how make ends:

cp src/cactus2hal.py ./bin//cactus2hal.py
chmod +x ./bin//cactus2hal.py
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/cactus2hal'
mkdir -p bin
ln -f submodules/cactus2hal/bin/* bin/
make[1]: Leaving directory `/home/tk19812/software/cactus'

[francicco]

I run the test:

cPecanRealign: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

[francicco]

Where is cPecanRealign generated? Maybe I can link the kyoto libs correctly F

[francicco]

I think I may have fix it. The example is running and it's not throwing me errors, so far...

Issued job 'CollateBlasts2' kind-CollateBlasts2/instancekm7znrh9 with job batch system ID: 153 and cores: 1, disk: 1.6 G, and memory: 2.0 G
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6bp08aat/worker_log.txt
Job ended: 'CollateBlasts2' kind-CollateBlasts2/instancekm7znrh9
Issued job 'CollateBlasts' kind-CollateBlasts/instancec0cq985v with job batch system ID: 154 and cores: 1, disk: 2.0 G, and memory: 2.0 G
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp685pjfif/worker_log.txt
Job ended: 'CollateBlasts' kind-CollateBlasts/instancec0cq985v
Issued job 'BlastIngroupsAndOutgroups' kind-BlastIngroupsAndOutgroups/instancegxv5h2q_ with job batch system ID: 155 and cores: 1, disk: 2.0 G, and memory: 2.0 G
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmpolsutm3k/worker_log.txt
Job ended: 'BlastIngroupsAndOutgroups' kind-BlastIngroupsAndOutgroups/instancegxv5h2q_
Issued job 'Job' kind-Job/instance0q9ds3dk with job batch system ID: 156 and cores: 0, disk: 100.0 M, and memory: 512.0 M
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmpkstuk2ci/worker_log.txt
Job ended: 'Job' kind-Job/instance0q9ds3dk
Issued job 'mappingQualityRescoring' kind-mappingQualityRescoring/instancejntblfz3 with job batch system ID: 157 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'updateExpWrapperForOutgroups' kind-updateExpWrapperForOutgroups/instance1afkzsow with job batch system ID: 158 and cores: 1, disk: 2.0 G, and memory: 2.0 G
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp3sud3ro5/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp2pl0xnfr/worker_log.txt
Job ended: 'updateExpWrapperForOutgroups' kind-updateExpWrapperForOutgroups/instance1afkzsow
Job ended: 'mappingQualityRescoring' kind-mappingQualityRescoring/instancejntblfz3
Issued job 'Job' kind-Job/instance0q9ds3dk with job batch system ID: 159 and cores: 0, disk: 100.0 M, and memory: 512.0 M
Got message from job at time 03-03-2020 18:58:27: Input cigar file has 7362 lines
Got message from job at time 03-03-2020 18:58:27: Filtered, non-overlapping primary cigar file has 11273 lines
Got message from job at time 03-03-2020 18:58:27: Filtered, non-overlapping secondary cigar file has 31711 lines
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmpqibb69ym/worker_log.txt
Job ended: 'Job' kind-Job/instance0q9ds3dk
Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance2pyh2xu8 with job batch system ID: 160 and cores: 1, disk: 2.0 G, and memory: 2.0 G
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmpvjhixzmm/worker_log.txt
Job ended: 'EncapsulatedJob' kind-EncapsulatedJob/instance2pyh2xu8
Issued job 'CactusSetupCheckpoint' kind-CactusSetupCheckpoint/instancem01k8k3e with job batch system ID: 161 and cores: 1, disk: 2.0 G, and memory: 3.3 G
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmppbl87k2w/worker_log.txt
Job ended: 'CactusSetupCheckpoint' kind-CactusSetupCheckpoint/instancem01k8k3e
Issued job 'StartPrimaryDB' kind-StartPrimaryDB/instancedko7vd1c with job batch system ID: 162 and cores: 1, disk: 2.0 G, and memory: 3.3 G
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmppjcfr7q_/worker_log.txt
Job ended: 'StartPrimaryDB' kind-StartPrimaryDB/instancedko7vd1c
Issued job 'KtServerService' kind-KtServerService/instancep_ey18_8 with job batch system ID: 163 and cores: 0, disk: 2.0 G, and memory: 2.3 G
INFO:toil.worker:Redirecting logging to /tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/worker_log.txt

[francicco]

there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port', '14271', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p']
ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

[diekhans]

Somehow you are still linking with shared libraries rather than the kyoto built by cactus.

Please start over; rather than set LDFLAGS, etc variables on the command line, please do them in:

include.local.mk

and set with export as show in the HDF5 example in the README.

Francesco Cicconardi notifications@github.com writes:

there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port', '14271', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p']
ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594116619 there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52. WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). INFO:cactus.shared.common:Running the command ['netstat', '-tuplen'] (No info could be read for "-p": geteuid()=432968 but you should be root.) INFO:cactus.shared.common:Running the command ['ktserver', '-port', '14271', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p'] ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

[francicco]

If I don't look them the make will fail F

On Tue, 3 Mar 2020, 19:20 Mark Diekhans, notifications@github.com wrote:

Somehow you are still linking with shared libraries rather than the kyoto built by cactus.

Please start over; rather than set LDFLAGS, etc variables on the command line, please do them in:

include.local.mk

and set with export as show in the HDF5 example in the README.

Francesco Cicconardi notifications@github.com writes:

there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version
3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be
root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port',
'14271', '-ls', '-tout', '200000', '-th', '64', '-bgs',
'/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot',
'-bgsc', 'lzo', '-bgsi', '1000000', '-log',
'/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp',
':#opts=ls#bnum=30m#msiz=50g#ktopts=p']
ktserver: error while loading shared libraries: libkyototycoon.so.2:
cannot open shared object file: No such file or directory

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub:

https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594116619 there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52. WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). INFO:cactus.shared.common:Running the command ['netstat', '-tuplen'] (No info could be read for "-p": geteuid()=432968 but you should be root.) INFO:cactus.shared.common:Running the command ['ktserver', '-port', '14271', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p'] ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ComparativeGenomicsToolkit/cactus/issues/103?email_source=notifications&email_token=ACEW6FSWVM7J6PYQ5DM4BPDRFVKARA5CNFSM4JAD64R2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENUZJLI#issuecomment-594121901, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEW6FRZQRUBHF25GFHSDZTRFVKARANCNFSM4JAD64RQ .

[diekhans]

Some will have to be added back in, but the problem is having things you don't need. So better to start with a clean environment and then add what you know you need. At least remove your own kyoto.

Also, adding them in include.local.mk keeps you from having to specify them if you have to recompile.

For instances, I have: export PKG_CONFIG_PATH=${MED_OPT}/lib/pkgconfig

Francesco Cicconardi notifications@github.com writes:

If I don't look them the make will fail F

On Tue, 3 Mar 2020, 19:20 Mark Diekhans, notifications@github.com wrote:

Somehow you are still linking with shared libraries rather than the kyoto built by cactus.

Please start over; rather than set LDFLAGS, etc variables on the command line, please do them in:

include.local.mk

and set with export as show in the HDF5 example in the README.

Francesco Cicconardi notifications@github.com writes:

there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version
3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be
root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port',
'14271', '-ls', '-tout', '200000', '-th', '64', '-bgs',
'/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot',
'-bgsc', 'lzo', '-bgsi', '1000000', '-log',
'/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp',
':#opts=ls#bnum=30m#msiz=50g#ktopts=p']
ktserver: error while loading shared libraries: libkyototycoon.so.2:
cannot open shared object file: No such file or directory

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub:

https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594116619 there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52. WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). INFO:cactus.shared.common:Running the command ['netstat', '-tuplen'] (No info could be read for "-p": geteuid()=432968 but you should be root.) INFO:cactus.shared.common:Running the command ['ktserver', '-port', '14271', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p'] ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

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-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594171673If I don't look them the make will fail F

On Tue, 3 Mar 2020, 19:20 Mark Diekhans, notifications@github.com wrote:

Somehow you are still linking with shared libraries rather than the kyoto built by cactus.

Please start over; rather than set LDFLAGS, etc variables on the command line, please do them in:

include.local.mk

and set with export as show in the HDF5 example in the README.

Francesco Cicconardi notifications@github.com writes:

there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version
3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be
root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port',
'14271', '-ls', '-tout', '200000', '-th', '64', '-bgs',
'/tmp/
toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/
tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot',
'-bgsc', 'lzo', '-bgsi', '1000000', '-log',
'/tmp/
toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/
tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp',
':#opts=ls#bnum=30m#msiz=50g#ktopts=p']
ktserver: error while loading shared libraries: libkyototycoon.so.2:
cannot open shared object file: No such file or directory

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub:

https://github.com/ComparativeGenomicsToolkit/cactus/issues/103# issuecomment-594116619 there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52. WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). INFO:cactus.shared.common:Running the command ['netstat', '-tuplen'] (No info could be read for "-p": geteuid()=432968 but you should be root.) INFO:cactus.shared.common:Running the command ['ktserver', '-port', '14271', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/ toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/ tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/ toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/ tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p'] ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

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[francicco]

I honestly don't understand what to do. Never modified the include.mk, no idea where to start with. It's all too frustrating for me. Why is it so complicated? Fuck! F

On Tue, 3 Mar 2020, 21:57 Mark Diekhans, notifications@github.com wrote:

Some will have to be added back in, but the problem is having things you don't need. So better to start with a clean environment and then add what you know you need. At least remove your own kyoto.

Also, adding them in include.local.mk keeps you from having to specify them if you have to recompile.

For instances, I have: export PKG_CONFIG_PATH=${MED_OPT}/lib/pkgconfig

Francesco Cicconardi notifications@github.com writes:

If I don't look them the make will fail F

On Tue, 3 Mar 2020, 19:20 Mark Diekhans, notifications@github.com wrote:

Somehow you are still linking with shared libraries rather than the kyoto built by cactus.

Please start over; rather than set LDFLAGS, etc variables on the command line, please do them in:

include.local.mk

and set with export as show in the HDF5 example in the README.

Francesco Cicconardi notifications@github.com writes:

there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version
3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from
os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from
os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be
root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port',
'14271', '-ls', '-tout', '200000', '-th', '64', '-bgs',

'/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log',

'/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p']

ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

--
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:

https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594116619

there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52. WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). INFO:cactus.shared.common:Running the command ['netstat', '-tuplen'] (No info could be read for "-p": geteuid()=432968 but you should be root.) INFO:cactus.shared.common:Running the command ['ktserver', '-port', '14271', '-ls', '-tout', '200000', '-th', '64', '-bgs',

'/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log',

'/tmp/toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p']

ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/ComparativeGenomicsToolkit/cactus/issues/103?email_source=notifications&email_token=ACEW6FSWVM7J6PYQ5DM4BPDRFVKARA5CNFSM4JAD64R2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENUZJLI#issuecomment-594121901 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ACEW6FRZQRUBHF25GFHSDZTRFVKARANCNFSM4JAD64RQ

.

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub:

https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594171673If I don't look them the make will fail F

On Tue, 3 Mar 2020, 19:20 Mark Diekhans, notifications@github.com wrote:

Somehow you are still linking with shared libraries rather than the kyoto built by cactus.

Please start over; rather than set LDFLAGS, etc variables on the command line, please do them in:

include.local.mk

and set with export as show in the HDF5 example in the README.

Francesco Cicconardi notifications@github.com writes:

there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version
3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from
os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from
os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be
root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port',
'14271', '-ls', '-tout', '200000', '-th', '64', '-bgs',
'/tmp/

toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/ tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot',

'-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/

toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/ tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp',

':#opts=ls#bnum=30m#msiz=50g#ktopts=p']

ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

--
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:

https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#
issuecomment-594116619
there's actually and error:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version
3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from
os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may
exist, but is not yet referenced by the worker (KeyError from
os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be
root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port',
'14271', '-ls', '-tout', '200000', '-th', '64', '-bgs',
'/tmp/

toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/ tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tnw6zi16y/snapshot',

'-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/

toil-ed5b990e-528a-4277-a016-9de3b412cb38-81657330c30e4f38a6b8e3469f401cce/ tmp6gfst5z2/2a2d1535-6e5b-4337-871e-b178afb8d363/tmpz504atgo.tmp',

':#opts=ls#bnum=30m#msiz=50g#ktopts=p']

ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/ComparativeGenomicsToolkit/cactus/issues/103?email_source =notifications&email_token=

ACEW6FSWVM7J6PYQ5DM4BPDRFVKARA5CNFSM4JAD64R2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENUZJLI

issuecomment-594121901>,

or unsubscribe https://github.com/notifications/unsubscribe-auth/ ACEW6FRZQRUBHF25GFHSDZTRFVKARANCNFSM4JAD64RQ .

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[francicco]

This is not very helpful at all F

[diekhans]

setting environment variables in make is a GNU make extension.

Try a fresh compile, only don't specify the kyoto options on the command line. To work around problems compiling kyoto we now include it as a static library.

[francicco]

I'm sorry I really don't understand what all that means! F

[francicco]

this is the first problem

checking lzo/lzo1x.h usability... no
checking lzo/lzo1x.h presence... no
checking for lzo/lzo1x.h... no
configure: error: lzo/lzo1x.h is required
make[2]: *** [kyotocabinet/Makefile] Error 1
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/kyoto'
make[1]: *** [suball.kyoto] Error 2
make[1]: Leaving directory `/home/tk19812/software/cactus'
make: *** [all] Error 2

How do I fix that? F

[francicco]

Second problem:

gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG   -I/usr/local/include -DHAVE_KYOTO_TYCOON=1     -I../externalTools/quicktree_1.1/include/  -I inc -I ../lib/  -c impl/*.c
g++  -O3 -g -Wall -funroll-loops -DNDEBUG  -I/usr/local/include -DHAVE_KYOTO_TYCOON=1     -I../externalTools/quicktree_1.1/include/  -I inc -I ../lib/ -c impl/*.cpp
impl/sonLibKVDatabase_KyotoTycoon.cpp:36:10: fatal error: /usr/local/include/ktremotedb.h: Permission denied
   36 | #include <ktremotedb.h>
      |          ^~~~~~~~~~~~~~
compilation terminated.

I need specific ways to fix these. I'm a fucking biologist, not a computer scientist! Unfortunately, the IT is not helping me with this, those fuckers! F

[diekhans]

please send command; you can attach files to the ticket, so all output would be good.

Francesco Cicconardi notifications@github.com writes:

this is the first problem

checking lzo/lzo1x.h usability... no
checking lzo/lzo1x.h presence... no
checking for lzo/lzo1x.h... no
configure: error: lzo/lzo1x.h is required
make[2]: *** [kyotocabinet/Makefile] Error 1
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/kyoto'
make[1]: *** [suball.kyoto] Error 2
make[1]: Leaving directory `/home/tk19812/software/cactus'
make: *** [all] Error 2

How do I fix that? F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594236986 this is the first problem

checking lzo/lzo1x.h usability... no checking lzo/lzo1x.h presence... no checking for lzo/lzo1x.h... no configure: error: lzo/lzo1x.h is required make[2]: [kyotocabinet/Makefile] Error 1 make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/kyoto' make[1]: [suball.kyoto] Error 2 make[1]: Leaving directory `/home/tk19812/software/cactus' make: *** [all] Error 2

How do I fix that? F

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[diekhans]

What kind of system are you running on?

Can you ask your admins to install software?

Now that kyoto is included in cactus, everything else should be available though common system packages.

[francicco]

Can you ask your admins to install software?

Do you think I didn't ask for? I did it in September: CACTUS + CAT. Here I am

What kind of system are you running on?

I don't know how to check.

Now that kyoto is included in cactus, everything else should be available though common system packages.

Now that I did what?

[francicco]

libkyototycoon.so.2 is not generated in the master branch of cactus. F

[diekhans]

It should be the static library, libkyototycoon.a

Francesco Cicconardi notifications@github.com writes:

libkyototycoon.so.2 is not generated in the master branch of cactus. F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594250384 libkyototycoon.so.2 is not generated in the master branch of cactus. F

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

[francicco]

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be root.)
INFO:cactus.shared.common:Running the command ['ktserver', '-port', '20546', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/toil-ea869cc4-a77a-4d2d-8181-ac4d6bb3a346-81657330c30e4f38a6b8e3469f401cce/tmpg71ywhlb/8f24a533-3c8a-4b6b-9451-915cdb0364fe/tyrlqwqqy/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/toil-ea869cc4-a77a-4d2d-8181-ac4d6bb3a346-81657330c30e4f38a6b8e3469f401cce/tmpg71ywhlb/8f24a533-3c8a-4b6b-9451-915cdb0364fe/tmpsaj9hfs5.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p']
ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

I'm sorry, but you're not very helpful. I'm going to sleep, it's 1AM here in the fucking UK.

F

[diekhans]

cactus and cat are not available in standard packages, however, the dependencies should be.

If you request HDF5 with C++ support it should bring in everything else you need, as long as you don't want phylop.

There is not one way to find out the linux distribution:

To find out what distribution of linux your running (Ex. Ubuntu) try lsb_release -a or cat /etc/release or cat /etc/issue or cat /proc/version.

Francesco Cicconardi notifications@github.com writes:

Can you ask your admins to install software?

Do you think I didn't ask for? I did it in September: CACTUS + CAT. Here I am

What kind of system are you running on?

I don't know how to check.

Now that kyoto is included in cactus, everything else should be available though common system packages.

Now that I did what?

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594249378 Can you ask your admins to install software?

Do you think I didn't ask for? I did it in September: CACTUS + CAT. Here I am

What kind of system are you running on?

I don't know how to check.

Now that kyoto is included in cactus, everything else should be available
though common system packages.

Now that I did what?

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[francicco]

(cactus_env) [tk19812@bp1-login01 cactus]$ lsb_release -a LSB Version: :core-4.1-amd64:core-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.6.1810 (Core) Release: 7.6.1810 Codename: Core

[diekhans]

You still have programs linked with the shared libraries

ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open

doing a make clean and then make without referencing another version kyoto should compile one with static libraries.

Sorry, this is research software built on a shoestring as well as stuff that requires years of C/C++ compiling experience.

Where in the UK? I work closely with EBI and spend a lot of time in Cambridge. If you are at EBI, I have a login.

Francesco Cicconardi notifications@github.com writes:

INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
INFO:cactus.shared.common:Running the command ['netstat', '-tuplen']
(No info could be read for "-p": geteuid()=432968 but you should be root.)
<> INFO:cactus.shared.common:Running the command ['ktserver', '-port', '20546', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/toil-ea869cc4-a77a-4d2d-8181-ac4d6bb3a346-81657330c30e4f38a6b8e3469f401cce/tmpg71ywhlb/8f24a533-3c8a-4b6b-9451-915cdb0364fe/tyrlqwqqy/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/toil-ea869cc4-a77a-4d2d-8181-ac4d6bb3a346-81657330c30e4f38a6b8e3469f401cce/tmpg71ywhlb/8f24a533-3c8a-4b6b-9451-915cdb0364fe/tmpsaj9hfs5.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p']
ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

I'm sorry, but you're not very helpful. I'm going to sleep, it's 1AM here in the fucking UK.

F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594253061 INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52. WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). WARNING:toil.resource:'JTRES_f20ff8f4eebf62a5e2b3753d513b39cb' may exist, but is not yet referenced by the worker (KeyError from os.environ[]). INFO:cactus.shared.common:Running the command ['netstat', '-tuplen'] (No info could be read for "-p": geteuid()=432968 but you should be root.) INFO:cactus.shared.common:Running the command ['ktserver', '-port', '20546', '-ls', '-tout', '200000', '-th', '64', '-bgs', '/tmp/toil-ea869cc4-a77a-4d2d-8181-ac4d6bb3a346-81657330c30e4f38a6b8e3469f401cce/tmpg71ywhlb/8f24a533-3c8a-4b6b-9451-915cdb0364fe/tyrlqwqqy/snapshot', '-bgsc', 'lzo', '-bgsi', '1000000', '-log', '/tmp/toil-ea869cc4-a77a-4d2d-8181-ac4d6bb3a346-81657330c30e4f38a6b8e3469f401cce/tmpg71ywhlb/8f24a533-3c8a-4b6b-9451-915cdb0364fe/tmpsaj9hfs5.tmp', ':#opts=ls#bnum=30m#msiz=50g#ktopts=p'] ktserver: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

I'm sorry, but you're not very helpful. I'm going to sleep, it's 1AM here in the fucking UK.

F

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[diekhans]

If you ask your admins to install these RPMs, it should be much easier: hdf5 hdf5-devel hdf5-static

Francesco Cicconardi notifications@github.com writes:

(cactus_env) [tk19812@bp1-login01 cactus]$ lsb_release -a LSB Version: :core-4.1-amd64:core-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.6.1810 (Core) Release: 7.6.1810 Codename: Core

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594253643 (cactus_env) [tk19812@bp1-login01 cactus]$ lsb_release -a LSB Version: :core-4.1-amd64:core-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.6.1810 (Core) Release: 7.6.1810 Codename: Core

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[francicco]

It looks like I fix it! Right? F

INFO:toil.worker:Redirecting logging to /tmp/toil-cb55f95d-e132-4449-9011-e10d0331704b-81657330c30e4f38a6b8e3469f401cce/tmpudrr7yht/worker_log.txt
Job ended: 'RunCactusPreprocessorThenProgressiveDown2' kind-RunCactusPreprocessorThenProgressiveDown2/instance7oqzg43h
Issued job 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instanceskrros47 with job batch system ID: 366 and cores: 1, disk: 2.0 G, and memory: 3.3 G
INFO:toil.worker:Redirecting logging to /tmp/toil-cb55f95d-e132-4449-9011-e10d0331704b-81657330c30e4f38a6b8e3469f401cce/tmpbj0yu0a2/worker_log.txt
Job ended: 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instanceskrros47
Finished toil run successfully.
Successfully deleted the job store: FileJobStore(/home/tk19812/software/cactus/jobStore)
Cactus has finished after 865.4396166829392 seconds

[diekhans]

hdf5-devel is needed for the header files. hdf5-static has the static libraries, not actually needed, however I always like to just ask for them at the same time in case I want to generate more portable programs

We put kyoto in as a submodule, as it was hard to get it on some systems. We intended to replace it with a more supported database.

Francesco Cicconardi notifications@github.com writes:

Dear Mark,

Sorry, this is research software built on a shoestring as well as stuff that requires years of C/C++ compiling experience.

I have years of experience with this kind of thing. I've been working with a number of different clusters with very little assistance. Last year, when I was in Cambridge (now I'm in Bristol) I manage to use both CACTUS and CAT. Now I moved to Bristol, and I have projects stated (using CACTUS and CAT) to finish. And that's probably why it's so frustrating. I understand it is complicated stuff to install and make it works, that's also the reason why I cannot do the scientist and the sys admin at the same time. These guys here seem very ... idle, to say the least, in doing their job. Anyway,

If you ask your admins to install these RPMs, it should be much easier: hdf5 hdf5-devel hdf5-static

hdf5 is definitely installed, maybe the devel and static are not. Why do I need the devel and static? I definitely installed kyoto libs in the previous installment in Cambridge.

These are the kyoto binaries that miss the links to the libraries: kttimedtest ktutilmgr ktutiltest ktutilserv kttimedmgr ktserver ktremotetest ktremotemgr

If I fix that the pipe line would work? Thanks a lot, and sorry my excesses (I'm italian ;) ).

Cheers F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594430616 Dear Mark,

Sorry, this is research software built on a shoestring as well as stuff that requires years of C/C++ compiling experience.

I have years of experience with this kind of thing. I've been working with a number of different clusters with very little assistance. Last year, when I was in Cambridge (now I'm in Bristol) I manage to use both CACTUS and CAT. Now I moved to Bristol, and I have projects stated (using CACTUS and CAT) to finish. And that's probably why it's so frustrating. I understand it is complicated stuff to install and make it works, that's also the reason why I cannot do the scientist and the sys admin at the same time. These guys here seem very ... idle, to say the least, in doing their job. Anyway,

If you ask your admins to install these RPMs, it should be much easier: hdf5 hdf5-devel hdf5-static

hdf5 is definitely installed, maybe the devel and static are not. Why do I need the devel and static? I definitely installed kyoto libs in the previous installment in Cambridge.

These are the kyoto binaries that miss the links to the libraries: kttimedtest ktutilmgr ktutiltest ktutilserv kttimedmgr ktserver ktremotetest ktremotemgr

If I fix that the pipe line would work? Thanks a lot, and sorry my excesses (I'm italian ;) ).

Cheers F

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[diekhans]

Looks good. Which cluster scheduler are you using? That is the next big challenge.

Francesco Cicconardi notifications@github.com writes:

It looks like I fix it!

[francicco]

The queueing system is PBSPro. Any tips for it? I need to align 60 genomes. F

[diekhans]

In general, the traditional batch systems don't work well in Toil and not one has implemented PBS. I don't know how hard it will be, probably hard. We got funding for Clouds, not HPC clusters, and now that funding is gone too :-(

What clades are you working with.

If you have a tree that is easy to decompose into subtrees and you have cluster nodes that have a fair about of memory and cores. you can split the alignment up and run each subtree on a node using multiple cores. Then the alignments can be merged at the end. I am working on instructions to do this.

The other option is to apply for AWS credits...

Francesco Cicconardi notifications@github.com writes:

The queueing system is PBSPro. Any tips for it? I need to align 60 genomes. F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594589140 The queueing system is PBSPro. Any tips for it? I need to align 60 genomes. F

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[francicco]

The clade I'm working with is the Heliconinii butterflies. On another cluster there's sbatch, is that better?

I have a tree. The idea is using busco genes to build the phylogeny. I already have, it's quite robust. We could decompose the whole dataset into clades, those are quite closely related, this splits are <10mya old. I'd be curious to know how to do it.

What about AWS credits? Anything with google instead? We would have some money to spend on it, but not a crazy amount.

F

[diekhans]

Butterflies!! Excellent. I am guess they have relatively small genomes. ~200 bird alignment was rather straight-forward in AWS; the 200 mammals almost killing a grad student.

sbatch is slurm and toil does work with it. Although it can be problematic. We need to watch it carefully. The main thing is to not overwhelm it with too many jobs or slurm can crash and make other users unhappy. I am working with someone else to do an alignment in SLURM.

AWS does give away credits for research, not sure what the current policy is. However, lets try with slurm first.

Google support in toil is weird. It has worked, but the object storage was in AWS, not at google. I would say it is poorly tested at best.

Francesco Cicconardi notifications@github.com writes:

The clade I'm working with is the Heliconinii butterflies. On another cluster there's sbatch, is that better?

I have a tree. The idea is using busco genes to build the phylogeny. I already have, it's quite robust. We could decompose the whole dataset into clades, those are quite closely related, this splits are <10mya old. I'd be curious to know how to do it.

What about AWS credits? Anything with google instead? We would have some money to spend on it, but not a crazy amount.

F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594792891 The clade I'm working with is the Heliconinii butterflies. On another cluster there's sbatch, is that better?

I have a tree. The idea is using busco genes to build the phylogeny. I already have, it's quite robust. We could decompose the whole dataset into clades, those are quite closely related, this splits are <10mya old. I'd be curious to know how to do it.

What about AWS credits? Anything with google instead? We would have some money to spend on it, but not a crazy amount.

F

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[francicco]

Ok, I'll talk with the IT here, and install CACTUS on the other cluster. For CAT would be the same? F

[diekhans]

Do your admins have to install it? Can you just run out of your home directory? That is what we do. Having to go through an install will slow things down if anything needs to be changed.

CAT is similar install to cactus, it needs several external programs from the UCSC browser group. There is a CAT annotation talk by the creator here friday and there is a dial-in, but that would be bad hours for you. I suspect he will be happy to share the slides.

Francesco Cicconardi notifications@github.com writes:

Ok, I'll talk with the IT here, and install CACTUS on the other cluster. For CAT would be the same? F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594862496 Ok, I'll talk with the IT here, and install CACTUS on the other cluster. For CAT would be the same? F

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[francicco]

Can I watch it remotely? don't care by the time. F

[francicco]

We have time to install CACTUS on the other cluster, I'm still finishing to assemble few genomes. F

[diekhans]

I will check, I am sure it will be fine.

Francesco Cicconardi notifications@github.com writes:

Can I watch it remotely? don't care by the time. F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594881255 Can I watch it remotely? don't care by the time. F

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[diekhans]

We have time to install CACTUS on the other cluster, I'm still finishing to assemble few genomes.

I am only concerned if there is a bug and we need to change the code. There isn't really an way to install cactus, except through docker. It just runs out of the tree you compiled it in.

Feel free to have your admins contract me about recommendations.

[francicco]

One IT said: "Toil/CACTUS should interface easily with both SLURM and PBS, the principles are the same , is is simply slight different commands. If you need help on the parameters to use, please just ask."

Can I have a typical script for cactus for SLURM? Or where I can find it?

Thanks F

Let me know for friday.

[diekhans]

Jobs are submitted dynamically by Toil. You could try running one of the test cases. https://toil.readthedocs.io/en/latest/gettingStarted/quickStart.html

The problem with the batch systems is that they generate single jobs rather than array jobs and cactus generates a lot of jobs.

Francesco Cicconardi notifications@github.com writes:

One IT said: "Toil/CACTUS should interface easily with both SLURM and PBS, the principles are the same , is is simply slight different commands. If you need help on the parameters to use, please just ask."

Can I have a typical script for cactus for SLURM? Or where I can find it?

Thanks F

Let me know for friday.

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-595140986 One IT said: "Toil/CACTUS should interface easily with both SLURM and PBS, the principles are the same , is is simply slight different commands. If you need help on the parameters to use, please just ask."

Can I have a typical script for cactus for SLURM? Or where I can find it?

Thanks F

Let me know for friday.

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[diekhans]

@francicco the CAT workshop will be on zoom:

https://ucsc.zoom.us/j/363140298

CAT Annotation Workshop - 9:00am - 11:45am Ian Fiddes' CAT Annotation Seminar - 12:00pm - 1:00pm CAT Annotation Workshop part 2 - 2:00pm - 5:00pm

Times are Pacific Standard Time (GMT-8)

[francicco]

Cool! I can make it. The first 2 for sure. F

[diekhans]

@francicco, the workshops had to be postponed due to illness

Ian believes your genomes are small enough that it should be doable on one system with sufficient cores and memory. This could be a cluster node.

This makes things much easier.

[francicco]

Yes, I talked with him a few hours ago. I'll give it a go. Tomorrow I'll talk with my boss and decide what to do. Thanks a lot Mark. Much appreciated! F

On Thu, 5 Mar 2020 at 21:00, Mark Diekhans notifications@github.com wrote:

@francicco, the workshops had to be postponed due to illness

Ian believes your genomes are small enough that it should be doable on one system with sufficient cores and memory. This could be a cluster node.

This makes things much easier.

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[francicco]

Hi @diekhans,

What this error about?

Using config from path /home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/cactus_progressive_config.xml.
('bkp55bd', True, False)
('bkp67ad', True, False)
('Anc15', False, False)
('bkp73bd', True, False)
('Anc12', False, False)
('bkp88bd', True, False)
('Anc09', False, False)
('wk44ad', True, False)
('wk59bd', True, False)
('Anc16', False, False)
('wk77bd', True, False)
('Anc13', False, False)
('wk86ad', True, False)
('Anc10', False, False)
('Anc07', False, False)
('wp45ad', True, False)
('wp45bd', True, False)
('Anc14', False, False)
('wp87bd', True, False)
('Anc11', False, False)
('wp96bd', True, False)
('Anc08', False, False)
('Anc06', False, False)
('Talp', True, False)
('Anc05', False, False)
('Timm', True, False)
('Anc03', False, False)
('Tbic', True, False)
('Tsim', True, False)
('Anc04', False, False)
('Anc02', False, False)
('Tpar', True, False)
('Anc01', False, False)
('Veme', True, True)
('Anc00', False, False)
['Anc15', 'Anc12', 'Anc09', 'Anc16', 'Anc13', 'Anc10', 'Anc07', 'Anc14', 'Anc11', 'Anc08', 'Anc06', 'Anc05', 'Anc03', 'Anc04', 'Anc02', 'Anc01', 'Anc00']
xmlRoot = <multi_cactus inputSequenceNames="Veme" inputSequences="/work/tk19812/TetramoriumProject/Genomes/V.emery_V1.0.fasta">
    <tree>Veme;</tree>
</multi_cactus>
Traceback (most recent call last):
  File "/home/tk19812/software/cactus/cactus_env/bin/cactus", line 8, in <module>
    sys.exit(main())
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 474, in main
    runCactusProgressive(options)
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 514, in runCactusProgressive
    cactusConfigID = toil.importFile(makeURL(project.getConfigPath()))
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/multiCactusProject.py", line 96, in getConfigPath
    return ExperimentWrapper(ET.parse(list(self.expMap.values())[0]).getroot()).getConfigPath()
IndexError: list index out of range

F

[diekhans]

Please attached your input file.

Francesco Cicconardi notifications@github.com writes:

Hi @diekhans,

What this error about?

Using config from path /home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/cactus_progressive_config.xml.
('bkp55bd', True, False)
('bkp67ad', True, False)
('Anc15', False, False)
('bkp73bd', True, False)
('Anc12', False, False)
('bkp88bd', True, False)
('Anc09', False, False)
('wk44ad', True, False)
('wk59bd', True, False)
('Anc16', False, False)
('wk77bd', True, False)
('Anc13', False, False)
('wk86ad', True, False)
('Anc10', False, False)
('Anc07', False, False)
('wp45ad', True, False)
('wp45bd', True, False)
('Anc14', False, False)
('wp87bd', True, False)
('Anc11', False, False)
('wp96bd', True, False)
('Anc08', False, False)
('Anc06', False, False)
('Talp', True, False)
('Anc05', False, False)
('Timm', True, False)
('Anc03', False, False)
('Tbic', True, False)
('Tsim', True, False)
('Anc04', False, False)
('Anc02', False, False)
('Tpar', True, False)
('Anc01', False, False)
('Veme', True, True)
('Anc00', False, False)
['Anc15', 'Anc12', 'Anc09', 'Anc16', 'Anc13', 'Anc10', 'Anc07', 'Anc14', 'Anc11', 'Anc08', 'Anc06', 'Anc05', 'Anc03', 'Anc04', 'Anc02', 'Anc01', 'Anc00']
xmlRoot = <multi_cactus inputSequenceNames="Veme" inputSequences="/work/tk19812/TetramoriumProject/Genomes/V.emery_V1.0.fasta">
  <tree>Veme;</tree>
</multi_cactus>
Traceback (most recent call last):
  File "/home/tk19812/software/cactus/cactus_env/bin/cactus", line 8, in <module>
    sys.exit(main())
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 474, in main
    runCactusProgressive(options)
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 514, in runCactusProgressive
    cactusConfigID = toil.importFile(makeURL(project.getConfigPath()))
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/multiCactusProject.py", line 96, in getConfigPath
    return ExperimentWrapper(ET.parse(list(self.expMap.values())[0]).getroot()).getConfigPath()
IndexError: list index out of range

F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-595995622 Hi @diekhans,

What this error about?

Using config from path /home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/cactus_progressive_config.xml. ('bkp55bd', True, False) ('bkp67ad', True, False) ('Anc15', False, False) ('bkp73bd', True, False) ('Anc12', False, False) ('bkp88bd', True, False) ('Anc09', False, False) ('wk44ad', True, False) ('wk59bd', True, False) ('Anc16', False, False) ('wk77bd', True, False) ('Anc13', False, False) ('wk86ad', True, False) ('Anc10', False, False) ('Anc07', False, False) ('wp45ad', True, False) ('wp45bd', True, False) ('Anc14', False, False) ('wp87bd', True, False) ('Anc11', False, False) ('wp96bd', True, False) ('Anc08', False, False) ('Anc06', False, False) ('Talp', True, False) ('Anc05', False, False) ('Timm', True, False) ('Anc03', False, False) ('Tbic', True, False) ('Tsim', True, False) ('Anc04', False, False) ('Anc02', False, False) ('Tpar', True, False) ('Anc01', False, False) ('Veme', True, True) ('Anc00', False, False) ['Anc15', 'Anc12', 'Anc09', 'Anc16', 'Anc13', 'Anc10', 'Anc07', 'Anc14', 'Anc11', 'Anc08', 'Anc06', 'Anc05', 'Anc03', 'Anc04', 'Anc02', 'Anc01', 'Anc00'] xmlRoot =

Veme;

Traceback (most recent call last): File "/home/tk19812/software/cactus/cactus_env/bin/cactus", line 8, in sys.exit(main()) File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 474, in main runCactusProgressive(options) File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 514, in runCactusProgressive cactusConfigID = toil.importFile(makeURL(project.getConfigPath())) File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/multiCactusProject.py", line 96, in getConfigPath return ExperimentWrapper(ET.parse(list(self.expMap.values())[0]).getroot()).getConfigPath() IndexError: list index out of range

F

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[francicco]

((((((((((bkp55bd:0.0001,bkp67ad:0.0001):0.0001,bkp73bd:0.0001):0.0001,bkp88bd:0.0001):0.0001,(((wk44ad:0.0001,wk59bd:0.0001):0.0001,wk77bd:0.0001):0.0001,wk86ad:0.0001):0.0001):0.0001,(((wp45ad:0.0001,wp45bd:0.0001):0.0001,wp87bd:0.0001):0.0001,wp96bd:0.0001):0.0001):0.0001,Talp:0.0001):0.0083,Timm:0.0061):0.0220,(Tbic:0.0240,Tsim:0.0219):0.0025):0.0030,Tpar:0.02811):0.0567,Veme:0.0891);
bkp55bd /work/tk19812/TetramoriumProject/Genomes/433_bkp55bd.fasta
bkp67ad /work/tk19812/TetramoriumProject/Genomes/433_bkp67ad.fasta
bkp73bd /work/tk19812/TetramoriumProject/Genomes/433_bkp73bd.fasta
bkp88bd /work/tk19812/TetramoriumProject/Genomes/433_bkp88bd.fasta
wk44ad /work/tk19812/TetramoriumProject/Genomes/433_wk44ad.fasta
wk59bd /work/tk19812/TetramoriumProject/Genomes/433_wk59bd.fasta
wk77bd /work/tk19812/TetramoriumProject/Genomes/433_wk77bd.fasta
wk86ad /work/tk19812/TetramoriumProject/Genomes/433_wk86ad.fasta
wp45ad /work/tk19812/TetramoriumProject/Genomes/433_wp45ad.fasta
wp45bd /work/tk19812/TetramoriumProject/Genomes/433_wp45bd.fasta
wp87bd /work/tk19812/TetramoriumProject/Genomes/433_wp87bd.fasta
wp96bd /work/tk19812/TetramoriumProject/Genomes/433_wp96bd.fasta
*Talp /work/tk19812/TetramoriumProject/Genomes/Talp.v2.0.assembly.fasta
Tbic /work/tk19812/TetramoriumProject/Genomes/Tbic.v1.0.assembly.fasta
Timm /work/tk19812/TetramoriumProject/Genomes/Timm.v1.0.assembly.fasta
Tpar /work/tk19812/TetramoriumProject/Genomes/Tpar.v1.0.assembly.fasta
Tsim /work/tk19812/TetramoriumProject/Genomes/Tsim.v1.0.assembly.fasta
*Veme /work/tk19812/TetramoriumProject/Genomes/V.emery_V1.0.fasta

[diekhans]

Would you make your fasta files available somewhere that I can download them?

My theory is you have an error in the input files that is not correctly detected by cactus, however I need to be able to reproduce it to fix.