SIGSEGV during Augustus PB step on test data

[laninsky]

Hi folks,

Apologies if I've missed something dumb during installation here, but I'm a bit stuck. I'm running cat on a slurm system, but using a single machine just to try and minimise complications:

luigi --module cat RunCat --hal=test_data/vertebrates.hal --ref-genome=mm10  --config=test_data/test.config --workDir /nesi/nobackup/uoo02424/bin/temp_test_work_dir --work-dir /nesi/nobackup/uoo02424/bin/test_work_dir --out-dir /nesi/nobackup/uoo02424/bin/test_out_dir  --augustus --augustus-cgp --augustus-pb --assembly-hub --binary-mode local --maxCores 5 --disableCaching --cleanWorkDir=never > log.txt

It seems to get through the Augustus CGP step fine, but then fails with a SIGSEGV on the Augustus PB step

10-29 05:20:22 luigi-interface INFO  [pid 31641] Worker Worker(salt=789703596, workers=1, host=wbn033, username=alana.alexander, pid=31641) running   ToilTask: AugustusPbDriverTask for hg38 using 
batchSystem singleMachine
10-29 05:20:25 cat   INFO  Launching AugustusPB toil pipeline on hg38.
10-29 05:20:27 toil.leader WARNING The job seems to have left a log file, indicating failure: 'augustus_pb_chunk' p/K/jobcYSQLG
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    INFO:toil:Running Toil version 3.18.0-84239d802248a5f4a220e762b3b8ce5cc92af0be.
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:'JTRES_d440cf64068fcb01605709db66d8e744' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    INFO:luigi-interface:Loaded ['/nesi/nobackup/uoo02424/bin/cat_luigi/luigi.cfg']
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:'JTRES_d440cf64068fcb01605709db66d8e744' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:Can't globalize module ModuleDescriptor(dirPath='/nesi/nobackup/uoo02424/bin/miniconda2/lib/python2.7/site-packages', name='toil.job', fromVirtualEnv=False).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:Can't globalize module ModuleDescriptor(dirPath='/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit', name='cat.augustus_pb', fromVirtualEnv=False).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:Can't globalize module ModuleDescriptor(dirPath='/nesi/nobackup/uoo02424/bin/miniconda2/lib/python2.7/site-packages', name='toil.job', fromVirtualEnv=False).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:Can't globalize module ModuleDescriptor(dirPath='/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit', name='cat.augustus_pb', fromVirtualEnv=False).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:Can't globalize module ModuleDescriptor(dirPath='/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit', name='cat.augustus_pb', fromVirtualEnv=False).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:Can't globalize module ModuleDescriptor(dirPath='/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit', name='cat.augustus_pb', fromVirtualEnv=False).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:'JTRES_d440cf64068fcb01605709db66d8e744' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:'JTRES_d440cf64068fcb01605709db66d8e744' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.resource:'JTRES_d440cf64068fcb01605709db66d8e744' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    Traceback (most recent call last):
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/nesi/nobackup/uoo02424/bin/miniconda2/lib/python2.7/site-packages/toil/worker.py", line 314, in workerScript
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/nesi/nobackup/uoo02424/bin/miniconda2/lib/python2.7/site-packages/toil/job.py", line 1351, in _runner
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        returnValues = self._run(jobGraph, fileStore)
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/nesi/nobackup/uoo02424/bin/miniconda2/lib/python2.7/site-packages/toil/job.py", line 1296, in _run
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        return self.run(fileStore)
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/nesi/nobackup/uoo02424/bin/miniconda2/lib/python2.7/site-packages/toil/job.py", line 1480, in run
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit/cat/augustus_pb.py", line 130, in augustus_pb_chunk
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        tools.procOps.run_proc(cmd, stdout=results)
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit/tools/procOps.py", line 60, in run_proc
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        pl.wait()
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit/tools/pipeline.py", line 1127, in wait
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        self.raiseIfExcept()
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit/tools/pipeline.py", line 1085, in raiseIfExcept
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        p.raiseIfExcept()
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG      File "/scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/Comparative-Annotation-Toolkit/tools/pipeline.py", line 749, in raiseIfExcept
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG        raise self.exceptInfo[0], self.exceptInfo[1], self.exceptInfo[2]
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    ProcException: process signaled: SIGSEGV: augustus --softmasking=1 --allow_hinted_splicesites=atac --alternatives-from-evidence=1 --UTR=1 --hintsfile=/nesi/nobackup/uoo02424/bin/temp_test_work_dir/toil-870fd876-08a7-4827-89c8-fd670c9d0bd2-a301ba27-672f-4856-ba5a-b6ec53983f3a/tmpsSFYBW/98d53963-ea74-4416-a1f3-538e1faac276/tmphdATE8.tmp --extrinsicCfgFile=/nesi/nobackup/uoo02424/bin/temp_test_work_dir/toil-870fd876-08a7-4827-89c8-fd670c9d0bd2-a301ba27-672f-4856-ba5a-b6ec53983f3a/tmpsSFYBW/98d53963-ea74-4416-a1f3-538e1faac276/tmpvtGP8k.tmp --species=human --/augustus/verbosity=0 --predictionStart=-0 --predictionEnd=-0 /scale_wlg_nobackup/filesets/nobackup/uoo02424/bin/temp_test_work_dir/toil-870fd876-08a7-4827-89c8-fd670c9d0bd2-a301ba27-672f-4856-ba5a-b6ec53983f3a/tmpsSFYBW/98d53963-ea74-4416-a1f3-538e1faac276/wbn033.40237.3604811865.tmp
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    ERROR:toil.worker:Exiting the worker because of a failed job on host wbn033
10-29 05:20:27 toil.leader WARNING p/K/jobcYSQLG    WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'augustus_pb_chunk' p/K/jobcYSQLG with ID p/K/jobcYSQLG to 1

...

Scheduled 187 tasks of which:
* 2 complete ones were encountered:
    - 1 EvaluateTransMap(...)
    - 1 Gff3ToAttrs(...)
* 79 ran successfully:
    - 1 AugustusCgp(...)
    - 1 BuildDb(...)
    - 1 Chaining(...)
    - 1 FakePsl(...)
    - 7 FilterTransMap(...)
    ...
* 8 failed:
    - 7 AugustusDriverTask(...)
    - 1 AugustusPbDriverTask(...)
* 98 were left pending, among these:
    * 98 had failed dependencies:
        - 7 AlignTranscriptDriverTask(...)
        - 1 AlignTranscripts(...)
        - 1 AssemblyHub(...)
        - 1 Augustus(...)
        - 1 AugustusPb(...)
        ...

This progress looks :( because there were failed tasks

Running the command outside of cat also gives a Segmentation Fault. From previous issues I thought filename length could be an issue, so I copied out the offending files and renamed them (also attached here with the modified names), but still ran into the same issue running it outside of cat:

augustus --softmasking=1 --allow_hinted_splicesites=atac --alternatives-from-evidence=1 --UTR=1 --hintsfile=test/hintsfile.tmp --extrinsicCfgFile=test/extrinsicCfgFile.tmp --species=human --/augustus/verbosity=0 --predictionStart=-0 --predictionEnd=-0 test/input.tmp

extrinsicCfgFile.tmp.txt
hintsfile.tmp.txt
input.tmp.txt

I followed the instructions for compiling Augustus CGP from https://github.com/Gaius-Augustus/Augustus (from yesterday or the day before's git version - I've tried getting cat installed multiple times over the last few weeks, so this was a fresh attempt), have used the pre-compiled kent binaries, and I'm using modules for Samtools (1.8), bamtools (2.4.1), bedtools (2.26.0). The only thing that seemed "off" during installation was that wiggletools failed some of its tests (however, a google suggested this could be because of reference mismatches between the bam and cram files):

Testing: ../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig
Testing: ../bin/wiggletools diff fixedStep.bw variableStep.wig fixedStep.wig
Trailing tokens: the last tokens in your command were not read, check your syntax:
... fixedStep.wig
Testing: ../bin/wiggletools do isZero diff fixedStep.bw fixedStep.wig
Testing: ../bin/wiggletools do isZero offset -1 ratio variableStep.bw variableStep.wig
Testing: ../bin/wiggletools do isZero diff bam.bam pileup.bg
Testing: ../bin/wiggletools do isZero diff bam.bam cram.cram
[E::cram_get_ref] Failed to populate reference for id 29
[E::cram_decode_slice] Unable to fetch reference #29 167..186835
[E::cram_next_slice] Failure to decode slice
[E::cram_get_ref] Failed to populate reference for id 42
[E::cram_decode_slice] Unable to fetch reference #42 466..29856
[E::cram_next_slice] Failure to decode slice
Traceback (most recent call last):
  File "test.py", line 37, in <module>
    assert test('../bin/wiggletools do isZero diff bam.bam cram.cram') == 0
AssertionError
make: *** [tests] Error 1

Any help would be really appreciated.

[ifiddes-10x-zz]

I have not encountered the wiggletools test data issues before, but I doubt it is a big deal. Wiggletools are only used for generating tracks for the final assembly hub, and so won't effect the actual annotation results.

Thank you for providing the input files to augustus! I just tried it myself using your input files and it seems to work fine.

augustus --softmasking=1 --allow_hinted_splicesites=atac --alternatives-from-evidence=1 --UTR=1 --hintsfile=hintsfile.tmp.txt --extrinsicCfgFile=extrinsicCfgFile.tmp.txt --species=human --/augustus/verbosity=0 --predictionStart=-0 --predictionEnd=-0 input.tmp.txt

I did this with a augustus binary compiled from commit 36ae43d6c7f. Do you know what commit you are on? I just pulled the most recent commit from the repo b8ce1b05d, recompiled and tried the above command again. I am also still not seeing a segfault. When you see the segfault, does it happen immediately or after a while?

Regardless, I think the next step is to open an issue on the augsutus repository with these inputs and with information about your build.

[laninsky]

Thanks for the super quick reply! I might try recompiling and giving it another go just in case something went awry. I'll let you know how it goes.

[ifiddes-10x-zz]

No worries, let me know how it goes. I did my test on a Ubuntu machine.

[laninsky]

===== Luigi Execution Summary =====

Scheduled 194 tasks of which:
* 194 ran successfully:
    - 7 AlignTranscriptDriverTask(...)
    - 1 AlignTranscripts(...)
    - 1 AssemblyHub(...)
    - 1 Augustus(...)
    - 1 AugustusCgp(...)
    ...

This progress looks :) because there were no failed tasks or missing dependencies

===== Luigi Execution Summary =====

Wooo! It does seem that it was something to do with difficulties in installing Augustus locally, because the cluster folks reinstalled an updated version and it worked. I'm going to attach my stream-of-consciousness of getting c-a-t installed below just in case it helps anyone else on an HPC system, and I'll post the Augustus easy build log on my issue over there. Thanks for all your help Ian!

# Installing miniconda2/python so we have pip to install c-a-t
bash modified_Minconda2.sh
chmod a+rwx miniconda2/bin/*
export PATH=/nesi/nobackup/uoo02424/bin/miniconda2/bin:$PATH

# install compilers for the other stuff we need to get together
module load gimkl/2017a

# Install pip and other conda requirements for dependencies
conda install pip

# install cat
git clone https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git
pip install -e Comparative-Annotation-Toolkit

# made a directory for the kent utilities
mkdir kent
cd kent

# Downloaded the kent utilities required by cat (see cat git) from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBed
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToFakePsl
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bamToPsl
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/transMapPslToGenePred
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslPosTarget
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/axtChain
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chainMergeSort
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslMap
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslRecalcMatch
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslMapPostChain
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslCheck
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslCDnaFilter
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/clusterGenes
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslToBigPsl
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedSort
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig

# Download blat in to same directory and add to path
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/FOOTER.txt
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer
chmod a+rwx *
export PATH=/nesi/nobackup/uoo02424/bin/kent:$PATH
cd ..

# Bedtools
module load BEDTools/2.26.0-gimkl-2017a 

# Samtools
module load SAMtools/1.8-gimkl-2017a

# Augustus
module load AUGUSTUS/3.3.2-gimkl-2017a

# The homGeneMapping program that is installed with the Augustus module doesn't have some of the options we need enabled
# so we will install it manually. We don't want to have to download the whole giant Augustus repository so we do:
svn export https://github.com/Gaius-Augustus/Augustus/trunk/auxprogs/homGeneMapping homGeneMapping
cd homGeneMapping
# We enable BOOST = true and SQLITE = true following https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit
# in the src/Makefile. We also hash out the clean lines in the main makefile, because we don't have the ../../bin folder it thinks it is going
# to copy the executable to. Then:
module load SQLite/3.16.2-gimkl-2017a
make
chmod a+rwx src/homGeneMapping
export PATH=/nesi/nobackup/uoo02424/bin/homGeneMapping/src:$PATH
cd ..

# Wiggletools and libBigWig dependency, back up in the "main" bin folder
git clone https://github.com/dpryan79/libBigWig.git
module load cURL/7.52.1-gimkl-2017a
cd libBigWig
make
chmod a+rwx *
export CPATH=/nesi/nobackup/uoo02424/bin/libBigWig:$CPATH
export LIBRARY_PATH=/nesi/nobackup/uoo02424/bin/libBigWig:$LIBRARY_PATH

cd ..
git clone https://github.com/Ensembl/WiggleTools.git
cd WiggleTools
make
# I do get errors when I try and run make test on bin/wiggletools, but i think this might be because HTS has updated to a different reference than the 
# cram file was based upon so I shall attempt to persist and see what happens. If there are weird wiggletools errors, we can probably blame this
export PATH=/nesi/nobackup/uoo02424/bin/WiggleTools/bin:$PATH
cd ..

# install sabamba
conda install -c bioconda sambamba

# install cactus because it has haltools that c-a-t depends on, and will have to align the genomes with something... it might as well be cactus.
#Back in main bin I cloned kyoto, which is a dependency of cactus
conda install lzo
export CPATH=/nesi/nobackup/uoo02424/bin/miniconda2/include:$CPATH
git clone https://github.com/carlosefr/kyoto.git
cd kyoto
module load lua/5.3.4
chmod -R a+rwx *
cd kyotocabinet
./configure --prefix=/nesi/nobackup/uoo02424/bin/kyototycoon
make
make install
export LIBRARY_PATH=/nesi/nobackup/uoo02424/bin/kyototycoon/lib:$LIBRARY_PATH
export CPATH=/nesi/nobackup/uoo02424/bin/kyototycoon/include:$CPATH
cd ..
make PREFIX=/nesi/nobackup/uoo02424/bin/kyototycoon
make install

# Then I went to the kyototycoon folder and into bin and:
chmod a+rwx *

# Add the  binaries to your path
export PATH=/nesi/nobackup/uoo02424/bin/kyototycoon/bin:$PATH

# We can now get rid of the installation folder from the main bin
rm -rf kyoto

# Cactus suggests we now have to do the following to get it to find kyoto
ttPrefix=/nesi/nobackup/uoo02424/bin/kyototycoon
export kyotoTycoonIncl="-I${ttPrefix}/include -DHAVE_KYOTO_TYCOON=1"
export kyotoTycoonLib="-L${ttPrefix}/lib -Wl,-rpath,${ttPrefix}/lib -lkyototycoon -lkyotocabinet -lz -lbz2 -lpthread -lm -lstdc++"

# That seemed to work, OK, now to Cactus's other dependencies:
git clone https://github.com/ComparativeGenomicsToolkit/cactus.git
cd cactus
pip install --upgrade .
git submodule update --init
chmod -R a+rwx *

# It seems easier to install some of the cactus's dependencies "manually". This meant the Makefile had to be modified before trying to make the file
# and some directories had to be removed
rm -rf submodules/hdf5
module load HDF5/1.8.18-gimkl-2017a

# Modifications to the cactus Makefile - pointing to a new direction for hc5++ on line 18
18 h5c++ = /opt/nesi/mahuika/HDF5/1.8.18-gimkl-2017a/bin/h5c++ 
# Removing referencs to the hdf5Rule on line 32
32 deps: ${libSonLib} ${libPinchesAndCacti} ${libMatchingAndOrdering} ${libCPecan} halRule
# Removing lines 74-78:
hdf5Rule: ${h5c++}
${h5c++}:
	@echo "Building dependency hdf5"
	@cd ${PWD}/submodules/hdf5 && (output=`(./configure --prefix=$(PWD)/submodules/hdf5 --enable-cxx && CFLAGS=-std=c99 AM_MAKEFLAGS=-e make -j4 -e && make install) 2>&1` || (echo "$$output"; exit 1))

# After tweaking this, make cactus by:
make

# Then in cactus's bin, we make everything executable:
chmod a+rwx bin/*

# We then have to add this to our path
export PATH=/nesi/nobackup/uoo02424/bin/cactus/bin:$PATH

## OK, to finally test run out cat we need to download the respository to get the test files we need out of it
cd Comparative-Annotation-Toolkit/
mv test_data ../
mv augustus_cfgs ../
mv *.cfg ../
cd ..
mkdir cat_luigi
mv *.cfg cat_luigi
export LUIGI_CONFIG_PATH=/nesi/nobackup/uoo02424/bin/cat_luigi/luigi.cfg
# Need to change the line in cat_luigi/luigi.cfg to point to the logging file e.g.
logging_conf_file = /nesi/nobackup/uoo02424/bin/cat_luigi/logging.cfg

# check cat module is all ready to go by
python
import cat
quit()

# Then to actually test (modify paths in test_data/test.config to be full absolute paths)
chmod -R a+rwx test_data/*

mkdir temp_test_work_dir

luigid --background --logdir luigi_logs

# Note that we have specified binary-mode local, so that c-a-t's dependencies are found on our path
# Also needed to specify maxDisk
luigi --module cat RunCat --hal=test_data/vertebrates.hal --ref-genome=mm10  --config=test_data/test.config --workDir /nesi/nobackup/uoo02424/bin/temp_test_work_dir --work-dir /nesi/nobackup/uoo02424/bin/test_work_dir --out-dir /nesi/nobackup/uoo02424/bin/test_out_dir  --augustus --augustus-cgp --augustus-pb --assembly-hub --binary-mode local --batchSystem singleMachine --maxCores 5 --disableCaching > log.txt


# When logging back in and/or running in submission script, make sure following are set/loaded:
module load gimkl/2017a
export PATH=/nesi/nobackup/uoo02424/bin/miniconda2/bin:$PATH
export PATH=/nesi/nobackup/uoo02424/bin/kent:$PATH
module load BEDTools/2.26.0-gimkl-2017a 
module load SAMtools/1.8-gimkl-2017a
module load AUGUSTUS/3.3.2-gimkl-2017a
module load SQLite/3.16.2-gimkl-2017a
export PATH=/nesi/nobackup/uoo02424/bin/homGeneMapping/src:$PATH
module load cURL/7.52.1-gimkl-2017a
export CPATH=/nesi/nobackup/uoo02424/bin/libBigWig:$CPATH
export LIBRARY_PATH=/nesi/nobackup/uoo02424/bin/libBigWig:$LIBRARY_PATH
export PATH=/nesi/nobackup/uoo02424/bin/WiggleTools/bin:$PATH
export CPATH=/nesi/nobackup/uoo02424/bin/miniconda2/include:$CPATH
module load lua/5.3.4
export LIBRARY_PATH=/nesi/nobackup/uoo02424/bin/kyototycoon/lib:$LIBRARY_PATH
export CPATH=/nesi/nobackup/uoo02424/bin/kyototycoon/include:$CPATH
export PATH=/nesi/nobackup/uoo02424/bin/kyototycoon/bin:$PATH
ttPrefix=/nesi/nobackup/uoo02424/bin/kyototycoon
export kyotoTycoonIncl="-I${ttPrefix}/include -DHAVE_KYOTO_TYCOON=1"
export kyotoTycoonLib="-L${ttPrefix}/lib -Wl,-rpath,${ttPrefix}/lib -lkyototycoon -lkyotocabinet -lz -lbz2 -lpthread -lm -lstdc++"
module load HDF5/1.8.18-gimkl-2017a
export PATH=/nesi/nobackup/uoo02424/bin/cactus/bin:$PATH
export LUIGI_CONFIG_PATH=/nesi/nobackup/uoo02424/bin/cat_luigi/luigi.cfg

[dandaman]

@laninsky thank you for sharing this! It helped a lot :-)

[laninsky]

Glad it helped @dandaman!