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+usage: cactus-pangenome [-h] [--config PATH] [--logCritical] [--logError] [--logWarning] [--logDebug] [--logInfo]
+ [--logOff]
+ [--logLevel {Critical,Error,Warning,Debug,Info,critical,error,warning,debug,info,CRITICAL,ERROR,WARNING,DEBUG,INFO}]
+ [--logFile LOGFILE] [--rotatingLogging] [--workDir PATH] [--coordinationDir PATH]
+ [--noStdOutErr] [--stats] [--clean {always,onError,never,onSuccess}]
+ [--cleanWorkDir {always,onError,never,onSuccess}] [--clusterStats [OPT_PATH]] [--restart]
+ [--batchSystem {aws_batch,single_machine,grid_engine,lsf,mesos,slurm,torque,htcondor,kubernetes}]
+ [--disableHotDeployment] [--disableAutoDeployment DISABLEAUTODEPLOYMENT]
+ [--maxJobs MAX_JOBS] [--maxLocalJobs MAX_LOCAL_JOBS] [--manualMemArgs]
+ [--runLocalJobsOnWorkers] [--coalesceStatusCalls] [--statePollingWait STATEPOLLINGWAIT]
+ [--batchLogsDir BATCH_LOGS_DIR] [--awsBatchRegion AWS_BATCH_REGION]
+ [--awsBatchQueue AWS_BATCH_QUEUE] [--awsBatchJobRoleArn AWS_BATCH_JOB_ROLE_ARN]
+ [--scale SCALE] [--dont_allocate_mem | --allocate_mem] [--symlinkImports BOOL]
+ [--moveOutputs BOOL] [--caching BOOL] [--provisioner {aws,gce,None}] [--nodeTypes NODETYPES]
+ [--maxNodes INT[,INT...]] [--minNodes INT[,INT...]] [--targetTime INT] [--betaInertia FLOAT]
+ [--scaleInterval INT] [--preemptibleCompensation FLOAT] [--nodeStorage INT]
+ [--nodeStorageOverrides NODETYPE:NODESTORAGE[,NODETYPE:NODESTORAGE...]] [--metrics BOOL]
+ [--assumeZeroOverhead BOOL] [--maxServiceJobs INT] [--maxPreemptibleServiceJobs INT]
+ [--deadlockWait INT] [--deadlockCheckInterval INT] [--defaultMemory DEFAULTMEMORY]
+ [--defaultCores FLOAT] [--defaultDisk INT]
+ [--defaultAccelerators ACCELERATOR[,ACCELERATOR...]] [--defaultPreemptible [BOOL]]
+ [--maxCores INT] [--maxMemory INT] [--maxDisk INT] [--retryCount INT]
+ [--enableUnlimitedPreemptibleRetries BOOL] [--doubleMem BOOL] [--maxJobDuration INT]
+ [--rescueJobsFrequency INT] [--maxLogFileSize MAXLOGFILESIZE] [--writeLogs [OPT_PATH]]
+ [--writeLogsGzip [OPT_PATH]] [--writeLogsFromAllJobs BOOL] [--writeMessages PATH]
+ [--realTimeLogging REALTIMELOGGING] [--disableChaining BOOL]
+ [--disableJobStoreChecksumVerification BOOL] [--sseKey PATH] [--setEnv NAME=VALUE or NAME]
+ [--servicePollingInterval FLOAT] [--forceDockerAppliance BOOL] [--statusWait INT]
+ [--disableProgress BOOL] [--debugWorker] [--disableWorkerOutputCapture] [--badWorker FLOAT]
+ [--badWorkerFailInterval FLOAT] --outDir OUTDIR --outName OUTNAME --reference REFERENCE
+ [REFERENCE ...] [--mgCores MGCORES] [--mgMemory MGMEMORY] [--mapCores MAPCORES]
+ [--delFilter DELFILTER] [--refContigs [REFCONTIGS ...]] [--otherContig OTHERCONTIG]
+ [--permissiveContigFilter [PERMISSIVECONTIGFILTER]] [--noSplit] [--maxLen MAXLEN]
+ [--consCores CONSCORES] [--consMemory CONSMEMORY] [--clip CLIP] [--filter FILTER]
+ [--gfa [GFA ...]] [--gbz [GBZ ...]] [--xg [XG ...]] [--odgi [ODGI ...]] [--viz [VIZ ...]]
+ [--draw [DRAW ...]] [--chrom-vg [CHROM_VG ...]] [--chrom-og [CHROM_OG ...]]
+ [--vcf [VCF ...]] [--vcfReference VCFREFERENCE [VCFREFERENCE ...]] [--vcfbub VCFBUB]
+ [--giraffe [GIRAFFE ...]] [--haplo [HAPLO ...]] [--indexCores INDEXCORES]
+ [--indexMemory INDEXMEMORY] [--chop [CHOP]] [--configFile CONFIGFILE] [--latest]
+ [--containerImage CONTAINERIMAGE] [--binariesMode {docker,local,singularity}]
+ jobStore seqFile
+
+positional arguments:
+ seqFile Seq file (will be modified if necessary to include graph Fasta sequence)
+
+options:
+ -h, --help show this help message and exit
+ --outDir OUTDIR Output directory
+ --outName OUTNAME Output name (without extension)
+ --reference REFERENCE [REFERENCE ...]
+ Reference event name(s). The first will be the "true" reference and will be left unclipped
+ and uncollapsed. It also should have been used with --reference in all upstream commands.
+ Other names will be promoted to reference paths in vg
+ --mgCores MGCORES Number of cores for minigraph construction (defaults to the same as --maxCores).
+ --mgMemory MGMEMORY Memory in bytes for the minigraph construction job (defaults to an estimate based on the
+ input data size). Standard suffixes like K, Ki, M, Mi, G or Gi are supported
+ (default=bytes))
+ --mapCores MAPCORES Number of cores for minigraph map. Overrides graphmap cpu in configuration
+ --delFilter DELFILTER
+ Filter out split-mapping-implied deletions > Nbp (default will be "delFilter" from the
+ config
+ --refContigs [REFCONTIGS ...]
+ Subset to these reference contigs (multiple allowed)
+ --otherContig OTHERCONTIG
+ Lump all reference contigs unselected by above options into single one with this name
+ --permissiveContigFilter [PERMISSIVECONTIGFILTER]
+ If specified, override the configuration to accept contigs so long as they have at least
+ given fraction of coverage (0.25 if no fraction specified). This can increase sensitivity of
+ very small, fragmented and/or diverse assemblies.
+ --noSplit Do not split by ref chromsome. This will require much more memory and potentially produce a
+ more complex graph
+ --maxLen MAXLEN Only align up to this many bases (overrides <bar bandingLimit> and <caf
+ maxRecoverableChainLength> in configuration)[default=10000]
+ --consCores CONSCORES
+ Number of cores for each cactus_consolidated job (defaults to all available / maxCores on
+ single_machine)
+ --consMemory CONSMEMORY
+ Memory in bytes for each cactus_consolidated job (defaults to an estimate based on the input
+ data size). Standard suffixes like K, Ki, M, Mi, G or Gi are supported (default=bytes))
+ --clip CLIP Generate clipped graph by removing anything longer than this amount that is unaligned to the
+ underlying minigraph. Set to 0 to disable (must also set --filter 0 as well).
+ [default=10000]
+ --filter FILTER Generate a frequency filtered graph (from the clipped graph) by removing any sequence
+ present in fewer than this many sequences. Set to 0 to disable. [default=2]
+ --gfa [GFA ...] Produce a GFA for given graph type(s) if specified. Valid types are 'full', 'clip', and
+ 'filter'. If no type specified 'clip' will be used ('full' used if clipping disabled).
+ Multiple types can be provided separated by a space. [--gfa clip assumed by default]
+ --gbz [GBZ ...] Generate GBZ/snarls indexes for the given graph type(s) if specified. Valid types are
+ 'full', 'clip' and 'filter'. If no type specified 'clip' will be used ('full' used if
+ clipping disabled). Multiple types can be provided separated by a space. --giraffe will also
+ produce these (and other) indexes
+ --xg [XG ...] Generate XG index (from GBZ) for the given graph type(s) if specified. Valid types are
+ 'full', 'clip' and 'filter'. If no type specified 'clip' will be used ('full' used if
+ clipping disabled). Multiple types can be provided separated by a space.
+ --odgi [ODGI ...] Generate ODGI (.og) versions for the given graph type(s) if specified. Valid types are
+ 'full', 'clip' and 'filter'. If no type specified 'full' will be used. Multiple types can be
+ provided separated by a space.
+ --viz [VIZ ...] Generate 1D ODGI visualizations of each chromosomal graph for the given graph type(s) if
+ specified. Valid types are 'full', 'clip' (but NOT `filter`). If no type specified 'full'
+ will be used. Multiple types can be provided separated by a space.
+ --draw [DRAW ...] Generate 2D ODGI visualizations of each chromosomal graph for the given graph type(s) if
+ specified. WARNING: EXPERIMENTAL OPTION. More work needs to be done to figure out the best
+ ODGI parameters to use, and it can be quite slow in the meantime. For larger graphs, use
+ --chrom-og and run the drawing by hand in order to avoid having draw issues prevent you from
+ getting the rest of your output. Valid types are 'full', 'clip' (but NOT `filter`). If no
+ type specified 'full' will be used. Multiple types can be provided separated by a space.
+ --chrom-vg [CHROM_VG ...]
+ Produce a directory of chromosomal graphs is vg format for the graph type(s) specified.
+ Valid typs are 'full', 'clip' and 'filter'. If no type specified 'clip' will be used ('full'
+ used if clipping disabled). Multiple types can be provided separated by a space. The output
+ will be the <outDir>/<outName>.chroms/ directory
+ --chrom-og [CHROM_OG ...]
+ Produce a directory of chromosomal graphs is odgi format for the graph type(s) specified.
+ Valid typs are 'full', 'clip' and 'filter'. If no type specified 'full' will be used.
+ Multiple types can be provided separated by a space. The output will be the
+ <outDir>/<outName>.chroms/ directory
+ --vcf [VCF ...] Generate a VCF from the given graph type(s). Valid types are 'full', 'clip' and 'filter'. If
+ no type specified, 'clip' will be used ('full' used if clipping disabled). Multipe types can
+ be provided separated by space
+ --vcfReference VCFREFERENCE [VCFREFERENCE ...]
+ If multiple references were provided with --reference, this option can be used to specify a
+ subset for vcf creation with --vcf. By default, --vcf will create VCFs for the first
+ reference only
+ --vcfbub VCFBUB Use vcfbub to flatten nested sites (sites with reference alleles > this will be replaced by
+ their children)). Setting to 0 will disable, only prudcing full VCF [default=100000].
+ --giraffe [GIRAFFE ...]
+ Generate Giraffe (.dist, .min) indexes for the given graph type(s). Valid types are 'full',
+ 'clip' and 'filter'. If not type specified, 'filter' will be used (will fall back to 'clip'
+ than full if filtering, clipping disabled, respectively). Multiple types can be provided
+ seperated by a space
+ --haplo [HAPLO ...] Generate haplotype subsampling (.ri, .hapl) indexes for the given graph type(s). Haplotype
+ subsampling is a new, better alternative filtering by allele frequency. Valid types are
+ 'full' and 'clip'. If not type specified, 'clip' will be used ('full' will be used if
+ clipping disabled). Multiple types can be provided seperated by a space. Must be used in
+ conjunction with --giraffe
+ --indexCores INDEXCORES
+ cores for general indexing and VCF constructions (defaults to the same as --maxCores)
+ --indexMemory INDEXMEMORY
+ Memory in bytes for each indexing and vcf construction job job (defaults to an estimate
+ based on the input data size). If specified will also be used to upper-bound per-chromosome
+ memory estimates -- ie no job will request more than this much memory.Standard suffixes like
+ K, Ki, M, Mi, G or Gi are supported (default=bytes))
+ --chop [CHOP] chop all graph nodes to be at most this long (default=1024 specified without value). By
+ default, nodes are only chopped for GBZ-derived formats, but left unchopped in the GFA, VCF,
+ etc. If this option is used, the GBZ and GFA should have consistent IDs
+ --configFile CONFIGFILE
+ Specify cactus configuration file
+ --latest Use the latest version of the docker container rather than pulling one matching this version
+ of cactus
+ --containerImage CONTAINERIMAGE
+ Use the the specified pre-built containter image rather than pulling one from quay.io
+ --binariesMode {docker,local,singularity}
+ The way to run the Cactus binaries
+
+ --config PATH Get options from a config file.
+
+Logging Options:
+ --logCritical Turn on loglevel Critical. Default: INFO.
+ --logError Turn on loglevel Error. Default: INFO.
+ --logWarning Turn on loglevel Warning. Default: INFO.
+ --logDebug Turn on loglevel Debug. Default: INFO.
+ --logInfo Turn on loglevel Info. Default: INFO.
+ --logOff Same as --logCRITICAL.
+ --logLevel {Critical,Error,Warning,Debug,Info,critical,error,warning,debug,info,CRITICAL,ERROR,WARNING,DEBUG,INFO}
+ Set the log level. Default: INFO. Options: ['Critical', 'Error', 'Warning', 'Debug', 'Info',
+ 'critical', 'error', 'warning', 'debug', 'info', 'CRITICAL', 'ERROR', 'WARNING', 'DEBUG',
+ 'INFO'].
+ --logFile LOGFILE File to log in.
+ --rotatingLogging Turn on rotating logging, which prevents log files from getting too big.
+
+Toil core options.:
+ Options to specify the location of the Toil workflow and turn on stats collation about the performance of jobs.
+
+ jobStore The location of the job store for the workflow. A job store holds persistent information
+ about the jobs, stats, and files in a workflow. If the workflow is run with a distributed
+ batch system, the job store must be accessible by all worker nodes. Depending on the desired
+ job store implementation, the location should be formatted according to one of the following
+ schemes: file:<path> where <path> points to a directory on the file systen
+ aws:<region>:<prefix> where <region> is the name of an AWS region like us-west-2 and
+ <prefix> will be prepended to the names of any top-level AWS resources in use by job store,
+ e.g. S3 buckets. google:<project_id>:<prefix> TODO: explain For backwards compatibility, you
+ may also specify ./foo (equivalent to file:./foo or just file:foo) or /bar (equivalent to
+ file:/bar).
+ --workDir PATH Absolute path to directory where temporary files generated during the Toil run should be
+ placed. Standard output and error from batch system jobs (unless --noStdOutErr is set) will
+ be placed in this directory. A cache directory may be placed in this directory. Temp files
+ and folders will be placed in a directory toil-<workflowID> within workDir. The workflowID
+ is generated by Toil and will be reported in the workflow logs. Default is determined by the
+ variables (TMPDIR, TEMP, TMP) via mkdtemp. This directory needs to exist on all machines
+ running jobs; if capturing standard output and error from batch system jobs is desired, it
+ will generally need to be on a shared file system. When sharing a cache between containers
+ on a host, this directory must be shared between the containers.
+ --coordinationDir PATH
+ Absolute path to directory where Toil will keep state and lock files.When sharing a cache
+ between containers on a host, this directory must be shared between the containers.
+ --noStdOutErr Do not capture standard output and error from batch system jobs.
+ --stats Records statistics about the toil workflow to be used by 'toil stats'.
+ --clean {always,onError,never,onSuccess}
+ Determines the deletion of the jobStore upon completion of the program. Choices: ['always',
+ 'onError', 'never', 'onSuccess']. The --stats option requires information from the jobStore
+ upon completion so the jobStore will never be deleted with that flag. If you wish to be able
+ to restart the run, choose 'never' or 'onSuccess'. Default is 'never' if stats is enabled,
+ and 'onSuccess' otherwise.
+ --cleanWorkDir {always,onError,never,onSuccess}
+ Determines deletion of temporary worker directory upon completion of a job. Choices:
+ ['always', 'onError', 'never', 'onSuccess']. Default = always. WARNING: This option should
+ be changed for debugging only. Running a full pipeline with this option could fill your disk
+ with excessive intermediate data.
+ --clusterStats [OPT_PATH]
+ If enabled, writes out JSON resource usage statistics to a file. The default location for
+ this file is the current working directory, but an absolute path can also be passed to
+ specify where this file should be written. This options only applies when using scalable
+ batch systems.
+
+Toil options for restarting an existing workflow.:
+ Allows the restart of an existing workflow
+
+ --restart If --restart is specified then will attempt to restart existing workflow at the location
+ pointed to by the --jobStore option. Will raise an exception if the workflow does not exist
+
+Toil options for specifying the batch system.:
+ Allows the specification of the batch system.
+
+ --batchSystem {aws_batch,single_machine,grid_engine,lsf,mesos,slurm,torque,htcondor,kubernetes}
+ The type of batch system to run the job(s) with, currently can be one of aws_batch,
+ single_machine, grid_engine, lsf, mesos, slurm, torque, htcondor, kubernetes. Default =
+ single_machine
+ --disableHotDeployment
+ Hot-deployment was renamed to auto-deployment. Option now redirects to
+ --disableAutoDeployment. Left in for backwards compatibility.
+ --disableAutoDeployment DISABLEAUTODEPLOYMENT
+ Should auto-deployment of Toil Python workflows be deactivated? If True, the workflow's
+ Python code should be present at the same location on all workers. Default = False.
+ --maxJobs MAX_JOBS Specifies the maximum number of jobs to submit to the backing scheduler at once. Not
+ supported on Mesos or AWS Batch. Use 0 for unlimited. Defaults to unlimited.
+ --maxLocalJobs MAX_LOCAL_JOBS
+ Specifies the maximum number of housekeeping jobs to run sumultaneously on the local system.
+ Use 0 for unlimited. Defaults to the number of local cores (128).
+ --manualMemArgs Do not add the default arguments: 'hv=MEMORY' & 'h_vmem=MEMORY' to the qsub call, and
+ instead rely on TOIL_GRIDGENGINE_ARGS to supply alternative arguments. Requires that
+ TOIL_GRIDGENGINE_ARGS be set.
+ --runLocalJobsOnWorkers, --runCwlInternalJobsOnWorkers
+ Whether to run jobs marked as local (e.g. CWLScatter) on the worker nodes instead of the
+ leader node. If false (default), then all such jobs are run on the leader node. Setting this
+ to true can speed up CWL pipelines for very large workflows with many sub-workflows and/or
+ scatters, provided that the worker pool is large enough.
+ --coalesceStatusCalls
+ Ask for job statuses from the batch system in a batch. Deprecated; now always enabled where
+ supported.
+ --statePollingWait STATEPOLLINGWAIT
+ Time, in seconds, to wait before doing a scheduler query for job state. Return cached
+ results if within the waiting period. Only works for grid engine batch systems such as
+ gridengine, htcondor, torque, slurm, and lsf.
+ --batchLogsDir BATCH_LOGS_DIR
+ Directory to tell the backing batch system to log into. Should be available on both the
+ leader and the workers, if the backing batch system writes logs to the worker machines'
+ filesystems, as many HPC schedulers do. If unset, the Toil work directory will be used. Only
+ works for grid engine batch systems such as gridengine, htcondor, torque, slurm, and lsf.
+ --awsBatchRegion AWS_BATCH_REGION
+ The AWS region containing the AWS Batch queue to submit to.
+ --awsBatchQueue AWS_BATCH_QUEUE
+ The name or ARN of the AWS Batch queue to submit to.
+ --awsBatchJobRoleArn AWS_BATCH_JOB_ROLE_ARN
+ The ARN of an IAM role to run AWS Batch jobs as, so they can e.g. access a job store. Must
+ be assumable by ecs-tasks.amazonaws.com.
+ --scale SCALE A scaling factor to change the value of all submitted tasks's submitted cores. Used in the
+ single_machine batch system. Useful for running workflows on smaller machines than they were
+ designed for, by setting a value less than 1. (default: 1)
+ --dont_allocate_mem A flag that can block allocating memory with '--mem' for job submissions on SLURM since some
+ system servers may reject any job request that explicitly specifies the memory allocation.
+ The default is to always allocate memory.
+ --allocate_mem A flag that can block allocating memory with '--mem' for job submissions on SLURM since some
+ system servers may reject any job request that explicitly specifies the memory allocation.
+ The default is to always allocate memory.
+
+Toil options for configuring storage.:
+ Allows configuring Toil's data storage.
+
+ --symlinkImports BOOL
+ When using a filesystem based job store, CWL input files are by default symlinked in.
+ Setting this option to True instead copies the files into the job store, which may protect
+ them from being modified externally. When set to False, as long as caching is enabled, Toil
+ will protect the file automatically by changing the permissions to read-only.default=True
+ --moveOutputs BOOL When using a filesystem based job store, output files are by default moved to the output
+ directory, and a symlink to the moved exported file is created at the initial location.
+ Setting this option to True instead copies the files into the output directory. Applies to
+ filesystem-based job stores only.default=False
+ --caching BOOL Enable or disable caching for your workflow, specifying this overrides default from job
+ store
+
+Toil options for autoscaling the cluster of worker nodes.:
+ Allows the specification of the minimum and maximum number of nodes in an autoscaled cluster, as well as
+ parameters to control the level of provisioning.
+
+ --provisioner {aws,gce,None}, -p {aws,gce,None}
+ The provisioner for cluster auto-scaling. This is the main Toil '--provisioner' option, and
+ defaults to None for running on single machine and non-auto-scaling batch systems. The
+ currently supported choices are ['aws', 'gce', None]. The default is None.
+ --nodeTypes NODETYPES
+ Specifies a list of comma-separated node types, each of which is composed of slash-separated
+ instance types, and an optional spot bid set off by a colon, making the node type
+ preemptible. Instance types may appear in multiple node types, and the same node type may
+ appear as both preemptible and non-preemptible. Valid argument specifying two node types:
+ c5.4xlarge/c5a.4xlarge:0.42,t2.large Node types: c5.4xlarge/c5a.4xlarge:0.42 and t2.large
+ Instance types: c5.4xlarge, c5a.4xlarge, and t2.large Semantics: Bid $0.42/hour for either
+ c5.4xlarge or c5a.4xlarge instances, treated interchangeably, while they are available at
+ that price, and buy t2.large instances at full price. default=[]
+ --maxNodes INT[,INT...]
+ Maximum number of nodes of each type in the cluster, if using autoscaling, provided as a
+ comma-separated list. The first value is used as a default if the list length is less than
+ the number of nodeTypes. default=[10]
+ --minNodes INT[,INT...]
+ Mininum number of nodes of each type in the cluster, if using auto-scaling. This should be
+ provided as a comma-separated list of the same length as the list of node types. default=[0]
+ --targetTime INT Sets how rapidly you aim to complete jobs in seconds. Shorter times mean more aggressive
+ parallelization. The autoscaler attempts to scale up/down so that it expects all queued jobs
+ will complete within targetTime seconds. default=1800
+ --betaInertia FLOAT A smoothing parameter to prevent unnecessary oscillations in the number of provisioned
+ nodes. This controls an exponentially weighted moving average of the estimated number of
+ nodes. A value of 0.0 disables any smoothing, and a value of 0.9 will smooth so much that
+ few changes will ever be made. Must be between 0.0 and 0.9. default=0.1
+ --scaleInterval INT The interval (seconds) between assessing if the scale of the cluster needs to change.
+ default=60
+ --preemptibleCompensation FLOAT, --preemptableCompensation FLOAT
+ The preference of the autoscaler to replace preemptible nodes with non-preemptible nodes,
+ when preemptible nodes cannot be started for some reason. This value must be between 0.0 and
+ 1.0, inclusive. A value of 0.0 disables such compensation, a value of 0.5 compensates two
+ missing preemptible nodes with a non-preemptible one. A value of 1.0 replaces every missing
+ pre-emptable node with a non-preemptible one. default=0.0
+ --nodeStorage INT Specify the size of the root volume of worker nodes when they are launched in gigabytes. You
+ may want to set this if your jobs require a lot of disk space. (default=50).
+ --nodeStorageOverrides NODETYPE:NODESTORAGE[,NODETYPE:NODESTORAGE...]
+ Comma-separated list of nodeType:nodeStorage that are used to override the default value
+ from --nodeStorage for the specified nodeType(s). This is useful for heterogeneous jobs
+ where some tasks require much more disk than others.
+ --metrics BOOL Enable the prometheus/grafana dashboard for monitoring CPU/RAM usage, queue size, and issued
+ jobs.
+ --assumeZeroOverhead BOOL
+ Ignore scheduler and OS overhead and assume jobs can use every last byte of memory and disk
+ on a node when autoscaling.
+
+Toil options for limiting the number of service jobs and detecting service deadlocks:
+ Allows the specification of the maximum number of service jobs in a cluster. By keeping this limited we can
+ avoid nodes occupied with services causing deadlocks.
+
+ --maxServiceJobs INT The maximum number of service jobs that can be run concurrently, excluding service jobs
+ running on preemptible nodes. default=9223372036854775807
+ --maxPreemptibleServiceJobs INT
+ The maximum number of service jobs that can run concurrently on preemptible nodes.
+ default=9223372036854775807
+ --deadlockWait INT Time, in seconds, to tolerate the workflow running only the same service jobs, with no jobs
+ to use them, before declaring the workflow to be deadlocked and stopping. default=60
+ --deadlockCheckInterval INT
+ Time, in seconds, to wait between checks to see if the workflow is stuck running only
+ service jobs, with no jobs to use them. Should be shorter than --deadlockWait. May need to
+ be increased if the batch system cannot enumerate running jobs quickly enough, or if polling
+ for running jobs is placing an unacceptable load on a shared cluster.default=30
+
+Toil options for cores/memory requirements.:
+ The options to specify default cores/memory requirements (if not specified by the jobs themselves), and to limit
+ the total amount of memory/cores requested from the batch system.
+
+ --defaultMemory DEFAULTMEMORY
+ The default amount of memory to request for a job. Only applicable to jobs that do not
+ specify an explicit value for this requirement. Standard suffixes like K, Ki, M, Mi, G or Gi
+ are supported. Default is 2.0 Gi.
+ --defaultCores FLOAT The default amount of cpu to request for a job. Only applicable to jobs that do not specify
+ an explicit value for this requirement. Fractions of a core (for example 0.1) are supported
+ on some batch systems [mesos, single_machine]. Default is 1.
+ --defaultDisk INT The default amount of disk to request for a job. Only applicable to jobs that do not specify
+ an explicit value for this requirement. Standard suffixes like K, Ki, M, Mi, G or Gi are
+ supported. Default is 2.0 Gi.
+ --defaultAccelerators ACCELERATOR[,ACCELERATOR...]
+ The default amount of accelerators to request for a job. Only applicable to jobs that do not
+ specify an explicit value for this requirement. Each accelerator specification can have a
+ type (gpu [default], nvidia, amd, cuda, rocm, opencl, or a specific model like nvidia-
+ tesla-k80), and a count [default: 1]. If both a type and a count are used, they must be
+ separated by a colon. If multiple types of accelerators are used, the specifications are
+ separated by commas. Default is [].
+ --defaultPreemptible [BOOL], --defaultPreemptable [BOOL]
+ Make all jobs able to run on preemptible (spot) nodes by default.
+ --maxCores INT The max amount of cpu to request for a job. Only applicable to jobs that do not specify an
+ explicit value for this requirement. Fractions of a core (for example 0.1) are supported on
+ some batch systems [mesos, single_machine]. Default is 9223372036854775807.
+ --maxMemory INT The max amount of memory to request for a job. Only applicable to jobs that do not specify
+ an explicit value for this requirement. Standard suffixes like K, Ki, M, Mi, G or Gi are
+ supported. Default is 8.0 Ei.
+ --maxDisk INT The max amount of disk to request for a job. Only applicable to jobs that do not specify an
+ explicit value for this requirement. Standard suffixes like K, Ki, M, Mi, G or Gi are
+ supported. Default is 8.0 Ei.
+
+Toil options for rescuing/killing/restarting jobs.:
+ The options for jobs that either run too long/fail or get lost (some batch systems have issues!).
+
+ --retryCount INT Number of times to retry a failing job before giving up and labeling job failed. default=1
+ --enableUnlimitedPreemptibleRetries BOOL, --enableUnlimitedPreemptableRetries BOOL
+ If set, preemptible failures (or any failure due to an instance getting unexpectedly
+ terminated) will not count towards job failures and --retryCount.
+ --doubleMem BOOL If set, batch jobs which die to reaching memory limit on batch schedulers will have their
+ memory doubled and they will be retried. The remaining retry count will be reduced by 1.
+ Currently supported by LSF.
+ --maxJobDuration INT Maximum runtime of a job (in seconds) before we kill it (this is a lower bound, and the
+ actual time before killing the job may be longer). default=9223372036854775807
+ --rescueJobsFrequency INT
+ Period of time to wait (in seconds) between checking for missing/overlong jobs, that is jobs
+ which get lost by the batch system. Expert parameter. default=60
+
+Toil log management options.:
+ Options for how Toil should manage its logs.
+
+ --maxLogFileSize MAXLOGFILESIZE
+ The maximum size of a job log file to keep (in bytes), log files larger than this will be
+ truncated to the last X bytes. Setting this option to zero will prevent any truncation.
+ Setting this option to a negative value will truncate from the beginning. Default=62.5 Ki
+ --writeLogs [OPT_PATH]
+ Write worker logs received by the leader into their own files at the specified path. Any
+ non-empty standard output and error from failed batch system jobs will also be written into
+ files at this path. The current working directory will be used if a path is not specified
+ explicitly. Note: By default only the logs of failed jobs are returned to leader. Set log
+ level to 'debug' or enable '--writeLogsFromAllJobs' to get logs back from successful jobs,
+ and adjust 'maxLogFileSize' to control the truncation limit for worker logs.
+ --writeLogsGzip [OPT_PATH]
+ Identical to --writeLogs except the logs files are gzipped on the leader.
+ --writeLogsFromAllJobs BOOL
+ Whether to write logs from all jobs (including the successful ones) without necessarily
+ setting the log level to 'debug'. Ensure that either --writeLogs or --writeLogsGzip is set
+ if enabling this option.
+ --writeMessages PATH File to send messages from the leader's message bus to.
+ --realTimeLogging REALTIMELOGGING
+ Enable real-time logging from workers to leader
+
+Toil miscellaneous options.:
+ Everything else.
+
+ --disableChaining BOOL
+ Disables chaining of jobs (chaining uses one job's resource allocation for its successor job
+ if possible).
+ --disableJobStoreChecksumVerification BOOL
+ Disables checksum verification for files transferred to/from the job store. Checksum
+ verification is a safety check to ensure the data is not corrupted during transfer.
+ Currently only supported for non-streaming AWS files.
+ --sseKey PATH Path to file containing 32 character key to be used for server-side encryption on
+ awsJobStore or googleJobStore. SSE will not be used if this flag is not passed.
+ --setEnv NAME=VALUE or NAME, -e NAME=VALUE or NAME
+ Set an environment variable early on in the worker. If VALUE is null, it will be looked up
+ in the current environment. Independently of this option, the worker will try to emulate the
+ leader's environment before running a job, except for some variables known to vary across
+ systems. Using this option, a variable can be injected into the worker process itself before
+ it is started.
+ --servicePollingInterval FLOAT
+ Interval of time service jobs wait between polling for the existence of the keep-alive flag.
+ Default: 60.0
+ --forceDockerAppliance BOOL
+ Disables sanity checking the existence of the docker image specified by TOIL_APPLIANCE_SELF,
+ which Toil uses to provision mesos for autoscaling.
+ --statusWait INT Seconds to wait between reports of running jobs.
+ --disableProgress BOOL
+ Disables the progress bar shown when standard error is a terminal.
+
+Toil debug options.:
+ Debug options for finding problems or helping with testing.
+
+ --debugWorker Experimental no forking mode for local debugging. Specifically, workers are not forked and
+ stderr/stdout are not redirected to the log.
+ --disableWorkerOutputCapture
+ Let worker output go to worker's standard out/error instead of per-job logs.
+ --badWorker FLOAT For testing purposes randomly kill --badWorker proportion of jobs using SIGKILL. default=0.0
+ --badWorkerFailInterval FLOAT
+ When killing the job pick uniformly within the interval from 0.0 to --badWorkerFailInterval
+ seconds after the worker starts. default=0.01
diff --git a/04_atelier_graphe_pangenome/mappingpoolseq2MC-PGG.md b/04_atelier_graphe_pangenome/MappingPoolSeq2MC-PGG.md
similarity index 100%
rename from 04_atelier_graphe_pangenome/mappingpoolseq2MC-PGG.md
rename to 04_atelier_graphe_pangenome/MappingPoolSeq2MC-PGG.md