Command line options
This page summarizes command line options for the Shasta executable.
We will make an effort to keep this page consistent with the code,
but discrepancies may temporarily appear
as we add new features. In that case, the list of command line options
obtained by invoking the Shasta executable with
--help is more authoritative than the contents
of this page.
Saving some typing
Many option names are long and descriptive. To make it easier to type them
Shasta provides the ability to create a bash completion script.
If you are using the bash shell
(the default shell in most modern Linux distributions),
you can use the commands below to save yourself some typing.
This assumes that the shasta executable is
named just like this - shasta - and is
accessible via your
PATH environment variable
(if it is not, you have to invoke shasta using
an absolute or relative path):
shasta --command createBashCompletionScript source shastaCompletion.shThe first command creates a script named
shastaCompletion.sh.
The second command runs that script in the current shell
(this is important - running the script without the source
command will not work).
Now, while typing a shasta option or keyword, you can press TAB, and the
option name will be completed as much as can be done
without ambiguity. You can also press TAB
a second time to get suggestions for what could be allowed next.
The command that generates the script can be run only once, but
you will need to rerun the source command above
every time you start a new shell. Alternatively, you can put the
source command in your .bashrc file
or in one of the standard locations used to store bash
completion scripts.
Options allowed only on the command line
| Option | Default value | Description |
|---|---|---|
--help or -h | Use this option to obtain a summary of allowed command line options. | |
--version or -v | Identify the Shasta version. | |
--config | Specifies the name of a pre-built configuration or a configuration file. This option has no default and is mandatory when running an assembly. | |
--input |
Specifies the names of the input files for the assembly.
This option is mandatory. At least one input file
must be specified. To specify multiple input files,
enter them separated by space after --input.
| |
--assemblyDirectory | ShastaRun |
Specifies the name of the directory where assembly
output is stored. If --command is assemble (the default), this directory must not exist and is automatically created.
For most other commands, this directory must exist.
See here
for more information on the output files
created by Shasta.
|
--command | assemble | Specifies the Shasta command to be run. |
--memoryMode(not supported on MacOS) | anonymous |
|
--memoryBacking(not supported on MacOS) | 4K |
|
--threads | 0 | Specifies the number of threads to be used, or 0 to request one thread per virtual processor. |
--suppressStdoutLog | false |
This is a
Boolean switch.
Normally, Shasta duplicates output to stdout
by sending a copy to stdout.log
in the assembly directory.
If this option is used, this behavior is suppressed, and
stdout.log is not created.
|
--exploreAccess | user |
Specifies access control for --command explore.
|
--port | 17100 |
The TCP port to be used for --command explore.
If the specified port is not available,
Shasta will try again after incrementing the port number a few times.
|
--alignmentsPafFile | "" |
The name of a PAF file containing alignments of reads to
a reference. Only used for --command explore,
for display of the alignment candidate graph. Experimental.
|
Options allowed on the command line and in a configuration file
See here for the format required to enter these options in a configuration file.
| Option | Default value | Description |
|---|---|---|
--Reads.representation | 1 | Read representation: 0 = raw sequence, 1 = Run-Length Encoded (RLE) sequence. Experimental. Do not use. |
--Reads.minReadLength | 10000 | Read length cutoff. Reads shorter than this number of bases are discarded on input and not used in the assembly. |
--Reads.desiredCoverage | 0 |
Specifies a desired value for total coverage, in bases.
If not zero, the read length cutoff specified via
--Reads.minReadLength is increased to reduce coverage
to the specified value.
This value can be specified as a number of bases,
or using power of 10 multipliers immediately following the numeric value.
The powers of ten can be abbreviated as
G, Gb, or Gbp for 109 bases,
M, Mb, or Mbp for 106 bases,
K, Kb, or Kbp for 103 bases.
For example, a desired coverage of 120×109 bases
can be requested specifying
120G, 120Gb, 120Gbp, or 120000000000.
If coverage available using only reads longer than Reads.minReadLength
is less than the value specified for --Reads.desiredCoverage,
the assembly terminates with an error message.
|
--Reads.noCache | False | This is a Boolean switch. If set, requests skipping the Linux cache when loading reads. Implemented for Linux only (uses the O_DIRECT flag). Can help performance, but only use it if you know you will not need to access the input files again soon. |
--Reads.palindromicReads.skipFlagging | False | Skip flagging palindromic reads. Oxford Nanopore reads should be flagged for better results. |
--Reads.palindromicReads.maxSkip | 100 | Same as Align.maxSkip but applied only to self reverse-complement alignments for the purpose of detecting palindromes. |
--Reads.palindromicReads.maxMarkerFrequency | 10 | Same as Align.maxMarkerFrequency but applied only to self reverse-complement alignments for the purpose of detecting palindromes. |
--Reads.palindromicReads.alignedFractionThreshold | 0.1 | Same as Align.maxMarkerFrequency but applied only to self reverse-complement alignments for the purpose of detecting palindromes. |
--Reads.palindromicReads.nearDiagonalFractionThreshold | 0.1 |
Count the fraction of markers within deltaThreshold (distance in markers)
from the diagonal and only flag reads above this fraction as palindromic.
|
--Reads.palindromicReads.deltaThreshold | 100 |
Used in combination with nearDiagonalFraction. This value defines how far from the diagonal
markers must be to be counted towards the nearDiagonalFraction. Unit is in markers.
|
--Kmers.generationMethod | 0 |
Used to select how k-mers to be used as markers are generated.
Can be one of the following:
|
--Kmers.k | 10 | Length of marker k-mers (in run-length representation). |
--Kmers.probability | 0.1 | Probability that a k-mer is selected to be used as a marker. |
--Kmers.enrichmentThreshold | 100. |
This controls the enrichment threshold above which k-mers
are considered overenriched.
Enrichment is ratio of k-mer frequency in reads to random.
Only used if --Kmers.generationMethod is 1 or 2.
|
--Kmers.distanceThreshold | 1000 |
Distance threshold, in RLE bases, for --Kmers.generationMethod 4.
Only used if --Kmers.generationMethod is 4.
|
--Kmers.file |
The absolute path of a file containing the k-mers
to be used as markers, one per line.
Only used if --Kmers.generationMethod is 3.
| |
--MinHash.version | 0 | The version of the MinHash/LowHash algorithm to be used. Can be 0 (default) or 1 (experimental). |
--MinHash.m | 4 | The number of consecutive markers that define a MinHash/LowHash feature. |
--MinHash.hashFraction | 0.01 | Defines how low a hash has to be to be used with the LowHash algorithm. |
--MinHash.minHashIterationCount | 10 | The number of MinHash/LowHash iterations, or 0 to let --MinHash.alignmentCandidatesPerRead control the number of iterations. |
--MinHash.alignmentCandidatesPerRead | 20 |
If --MinHash.minHashIterationCount is 0,
MinHash iteration is stopped when the average number of alignment candidates
that each read is involved in reaches this value.
If --MinHash.minHashIterationCount is not 0, this is not used.
|
--MinHash.minBucketSize | 0 | The minimum size for a bucket to be used by the MinHash/LowHash algoritm. |
--MinHash.maxBucketSize | 10 | The maximum size for a bucket to be used by the MinHash/LowHash algoritm. |
--MinHash.minFrequency | 2 | The minimum number of times a pair of reads must be found by the MinHash/LowHash algorithm in order to be considered a candidate alignment. |
--MinHash.allPairs | False | This is a Boolean switch that causes the MinHash process to be skipped. Instead, all possible read pairs are marked as alignment candidates, on both relative orientations. This should only be used for very small test assemblies as it can become prohibitively slow for large assemblies. |
--Align.alignMethod | 3 |
The alignment method to be used to compute marker alignments between reads:
|
--Align.maxSkip | 30 | The maximum number of markers that an alignment is allowed to skip. |
--Align.maxSkip | 30 | The maximum amount of marker drift that an alignment is allowed to tolerate between successive markers. |
--Align.maxTrim | 30 | The maximum number of skipped markers tolerated in an alignment at the beginning and end of a read. |
--Align.maxMarkerFrequency | 10 | Marker frequency threshold when computing alignments. Markers that occur more than this number of times in either of the two reads to be aligned are ignored. |
--Align.minAlignedMarkerCount | 100 | The minimum number of aligned markers for an alignment to be used. |
--Align.minAlignedFraction | 0 | The minimum fraction of aligned markers for an alignment to be used. |
--Align.matchScore | 6 | Match score for marker alignments (only for alignment methods 1 and 3). |
--Align.mismatchScore | -1 | Mismatch score for marker alignments (only for alignment methods 1 and 3). |
--Align.gapScore | -1 | Gap score for marker alignments (only for alignment methods 1 and 3). |
--Align.downsamplingFactor | 0.1 | Downsampling factor for downsampled marker alignments (only for alignment method 3). |
--Align.bandExtend | 10 | Amount to extend the alignment band, in markers (only used for alignment method 3). |
--Align.maxBand | 1000 | Maximum band width, in markers, for banded marker alignments (only used for alignment method 3). |
--Align.sameChannelReadAlignment.suppressDeltaThreshold | 0 |
If not zero, alignments between reads from the same nanopore channel
and close in time are suppressed. The read meta data fields
from the FASTA or FASTQ header are checked. If their difference, in
absolute value, is less than the value of this option, the alignment
is suppressed. This can help avoid assembly artifact.
This check is only done if the two reads have identical metadata fields
runid, sampleid, and ch.
If any of these metadata fields are missing, this check is suppressed and this
option has no effect.
|
--Align.suppressContainments | False | This is a Boolean switch. If set, containment alignments are suppressed. Containment alignments are alignments in which one read is entirely contained in another read, except possibly for up to maxTrim markers at the beginning and end. |
--Align.align4.deltaX | 200 | Only used for alignment method 4 (experimental). |
--Align.align4.deltaY | 10 | Only used for alignment method 4 (experimental). |
--Align.align4.minEntryCountPerCell | 10 | Only used for alignment method 4 (experimental). |
--Align.align4.maxDistanceFromBoundary | 100 | Only used for alignment method 4 (experimental). |
--ReadGraph.creationMethod | 0 | The method used to create the read graph (0 or 2). |
--ReadGraph.maxAlignmentCount | 6 | The maximum alignments to be kept in the read graph for each read. |
--ReadGraph.maxChimericReadDistance | 2 | Used for chimeric read detection. |
--ReadGraph.strandSeparationMethod | 1 |
Strand separation method. Spwecify one of the following values:
|
--ReadGraph.crossStrandMaxDistance | False | Maximum distance (edges) for strand separation method 1. |
--ReadGraph.removeConflicts | False | This is a Boolean switch. Remove conflicts from the read graph. Experimental - do not use. |
--ReadGraph.markerCountPercentile
| 0.015 |
Percentile for adaptive selection of --ReadGraph. markerCount
(only used when --ReadGraph.creationMethod is 2).
|
--ReadGraph.alignedFractionPercentile
| 0.12 |
Percentile for adaptive selection of --ReadGraph.alignedFraction
(only used when --ReadGraph.creationMethod is 2).
|
--ReadGraph.maxSkipPercentile
| 0.12 |
Percentile for adaptive selection of --ReadGraph.maxSkip
(only used when --ReadGraph.creationMethod is 2).
|
--ReadGraph.maxDriftPercentile
| 0.12 |
Percentile for adaptive selection of --ReadGraph.maxDrift
(only used when --ReadGraph.creationMethod is 2).
|
--ReadGraph.maxTrimPercentile
| 0.015 |
Percentile for adaptive selection of --ReadGraph.maxTrim
(only used when --ReadGraph.creationMethod is 2).
|
--ReadGraph.flagInconsistentAlignments | False | This is a Boolean switch. Flag inconsistent alignments. Experimental. |
--ReadGraph.flagInconsistentAlignments.triangleErrorThreshold | 200 |
Triangle error threshold, in markers, for flagging inconsistent alignments.
Only used if --ReadGraph.flagInconsistentAlignments is set. Experimental.
|
--ReadGraph.flagInconsistentAlignments.leastSquareErrorThreshold | 200 |
Least square error threshold, in markers, for flagging inconsistent alignments.
Only used if --ReadGraph.flagInconsistentAlignments is set. Experimental.
|
--ReadGraph.flagInconsistentAlignments.leastSquareMaxDistance | 1 |
Least square max distance for flagging inconsistent alignments.
Only used if --ReadGraph.flagInconsistentAlignments is set. Experimental.
|
--MarkerGraph.minCoverage | 10 | The minimum coverage for a marker graph vertex. Vertices with lower coverage are not generated. Specifying 0 causes a suitable value of this parameter to be selected automatically. |
--MarkerGraph.maxCoverage | 100 | The maximum coverage for a marker graph vertex. Vertices with higher coverage are not generated. |
--MarkerGraph.minCoveragePerStrand | 0 | The minimum coverage per strand for a marker graph vertex. Vertices with lower coverage on either strand are not generated. |
--MarkerGraph.minEdgeCoverage | 6 |
Minimum edge coverage (number of supporting oriented reads)
for a marker graph edge to be created.
Only used with --Assembly.mode 2.
|
--MarkerGraph.minEdgeCoveragePerStrand | 2 |
Minimum edge coverage (number of supporting oriented reads)
on each strand for a marker graph edge to be created.
Experimental. Only used with --Assembly.mode 2.
|
--MarkerGraph.allowDuplicateMarkers | False | This is a Boolean switch. It specifies whether to allow more than one marker on the same oriented read on a single marker graph vertex. Experimental. |
--MarkerGraph.cleanupDuplicateMarkers | False | This is a Boolean switch. It specifies whether to clean up marker graph vertices with more than one marker on the same oriented read. Experimental. |
--MarkerGraph.duplicateMarkersPattern1Threshold | 0.5 | Used when cleaning up marker graph vertices with more than one marker on the same oriented read. Experimental. |
--MarkerGraph.lowCoverageThreshold | 0 | Used during approximate transitive reduction. Edges with coverage less than or equal to this value are unconditionally removed from the marker graph, even at the cost of breaking reachability. This never happens with the default value 0. |
--MarkerGraph.highCoverageThreshold | 256 | Used during approximate transitive reduction. Edges with coverage greater than or equal to this value are unconditionally kept in the marker graph, even if they could be removed without breaking reachability. This never happens with the default value 256, because marker graph edge coverage is stored in one byte and saturates at 255. |
--MarkerGraph.maxDistance | 30 | Used during approximate transitive reduction of the marker graph. It controls the length of each Breadth First Search (BFS) used to determine reachability. This length is expressed in marker graph edges. |
--MarkerGraph.edgeMarkerSkipThreshold | 100 | Used during approximate transitive reduction of the marker graph. Edges with coverage 1 are unconditionally removed from the marker graph if the only supporting read has a marker skip of more than this number of markers on that edge. Large marker skips are indicative of artifacts or errors. |
--MarkerGraph.pruneIterationCount | 6 | The number of marker graph prune iterations. This equals the maximum length of dead branches that are removed. |
--MarkerGraph.simplifyMaxLength | 10,100,1000 | Used for bubble removal. |
--MarkerGraph.crossEdgeCoverageThreshold | 0. | Experimental. Cross edge coverage threshold. If this is not zero, assembly graph cross-edges with average edge coverage less than this value are removed, together with the corresponding marker graph edges. A cross edge is defined as an edge v0->v1 with out-degree(v0)>1, in-degree(v1)>1. |
--MarkerGraph.reverseTransitiveReduction | False | This is a Boolean switch. If set, approximate reverse transitive reduction of the marker graph in the reverse direction is also performed. |
--MarkerGraph.peakFinder.minAreaFraction | 0.08 |
Used in the automatic selection of
--MarkerGraph.minCoverage when --MarkerGraph.minCoverage is set to 0.
|
--MarkerGraph.peakFinder.areaStartIndex | 2 |
Used in the automatic selection of
--MarkerGraph.minCoverage when --MarkerGraph.minCoverage is set to 0.
|
--MarkerGraph.secondaryEdges.maxSkip | 1000000 | Maximum number of markers skipped by a secondary edge (mode 2 assembly only). |
--MarkerGraph.secondaryEdges.split.errorRateThreshold | 0.25 | Error rate threshold used for splitting secondary edges (mode 2 assembly only). |
--MarkerGraph.secondaryEdges.split.minCoverage | 4 | Minimum coverage for secondary edges generated during splitting (mode 2 assembly only). |
--Assembly.mode
| 0 | Assembly mode (0 = haploid assembly, 2 = phased diploid assembly). |
--Assembly.markerGraphEdgeLengthThresholdForConsensus
| 0 | Controls assembly of long marker graph edges. |
--Assembly.consensusCaller
| Modal | Used to select the consensus caller for repeat counts. |
--Assembly.storeCoverageData | False |
This is a
Boolean switch
used to request storing of coverage data (only useful in conjunction with --memoryMode filesystem).
|
--Assembly.writeReadsByAssembledSegment | False | This is a Boolean switch used to request writing a csv file containing all the reads that were used to assemble each segment). |
--Assembly.pruneLength | 0 | Prune length (in markers) for pruning of the assembly graph. Assembly graph leaves shorter than this number of markers are iteratively pruned. Set to zero to suppress pruning of the assembly graph. Assembly graph pruning takes place separately and in addition to marker graph pruning. |
--Assembly.detangleMethod | 0 |
Method used to detangle the assembly graph. Valid values:
|
--Assembly.detangle.diagonalReadCountMin | 1 |
Experimental. Minimum number of reads on detangle matrix diagonal elements required for detangling. Only used with
--Assembly.detangleMethod 2.
|
--Assembly.detangle.offDiagonalReadCountMax | 2 |
Experimental. Maximum number of reads on detangle matrix off-diagonal elements allowed for detangling. Only used with
--Assembly.detangleMethod 2.
|
--Assembly.detangle.offDiagonalRatio | 0.3 |
Experimental. Maximum ratio of total off-diagonal elements over diagonal element allowed for detangling. Only used with
--Assembly.detangleMethod 2.
|
--Assembly.iterative | False | This is a Boolean switch used to request iterative assembly (experimental). |
--Assembly.iterative.iterationCount | 3 | Number of iterations for iterative assembly (experimental). |
--Assembly.iterative.pseudoPathAlignMatchScore | 1 | Pseudopath alignment match score for iterative assembly (experimental). |
--Assembly.iterative.pseudoPathAlignMismatchScore | -1 | Pseudopath alignment mismatch score for iterative assembly (experimental). |
--Assembly.iterative.pseudoPathAlignGapScore | -1 | Pseudopath alignment gap score for iterative assembly (experimental). |
--Assembly.iterative.mismatchSquareFactor | 3. | Mismatch square factor for iterative assembly (experimental). |
--Assembly.iterative.minScore | 0. | Minimum pseudo-alignment score for iterative assembly (experimental). |
--Assembly.iterative.maxAlignmentCount | 6 | Maximum number of read graph neighbors for iterative assembly (experimental). |
--Assembly.iterative.bridgeRemovalIterationCount | 3 | Number of read graph bridge removal iterations for iterative assembly (experimental). |
--Assembly.iterative.bridgeRemovalMaxDistance | 2 | Maximum distance for read graph bridge removal for iterative assembly (experimental). |
--Assembly.mode2.strongBranchThreshold
| 2 | Minimum number of supporting reads required for a strong branch. Mode 2 assembly only. |
--Assembly.mode2.epsilon
| 0.1 | Epsilon for the Bayesian model used for phasing and bubble removal. This is the probability that a read appears on the wrong branch of a diploid bubble. Mode 2 assembly only. |
--Assembly.mode2.bubbleRemoval.minConcordantReadCount
| 3 | Minimum number of concordant reads for bubble removal. Mode 2 assembly only. |
--Assembly.mode2.bubbleRemoval.maxDiscordantReadCount
| 6 | Maximum number of discordant reads for bubble removal. Mode 2 assembly only. |
--Assembly.mode2.bubbleRemoval.minLogP
| 30 | Minimum log(P) (in decibels) for bubble removal. Mode 2 assembly only. |
--Assembly.mode2.bubbleRemoval.componentSizeThreshold
| 10 | Component size threshold for bubble removal. Mode 2 assembly only. |
--Assembly.mode2.phasing.minConcordantReadCount
| 2 | Minimum number of concordant reads for phasing. Mode 2 assembly only. |
--Assembly.mode2.phasing.maxDiscordantReadCount
| 1 | Maximum number of discordant reads for phasing. Mode 2 assembly only. |
--Assembly.mode2.phasing.minLogP | 10 | Minimum log(P) (in decibels) for phasing. Mode 2 assembly only. |
--Assembly.mode2.superbubble.maxSize
| 50 | Maximum size (number of edges) of a superbubble to be processed. Mode 2 assembly only. |
--Assembly.mode2.superbubble.maxChunkSize
| 20 | Maximum size (number of edges) of a superbubble chunk to be processed. Mode 2 assembly only. |
--Assembly.mode2.superbubble.edgeLengthThreshold
| 6 | Edge length threshold in markers for superbubble removal. Mode 2 assembly only. |
--Assembly.mode2.suppressGfaOutput
| False | This is a Boolean switch. If set, all GFA output is suppressed. Mode 2 assembly only. |
--Assembly.mode2.suppressFastaOutput
| False | This is a Boolean switch. If set, all FASTA output is suppressed. Mode 2 assembly only. |
--Assembly.mode2.suppressDetailedOutput
| False | This is a Boolean switch. If set, output of the detailed representation of the assembly is suppressed. Mode 2 assembly only. |
--Assembly.mode2.suppressPhasedOutput
| False | This is a Boolean switch. If set, output of the phased representation of the assembly is suppressed. Mode 2 assembly only. |
--Assembly.mode2.suppressHaploidOutput
| False | This is a Boolean switch. If set, output of the haploid representation of the assembly is suppressed. Mode 2 assembly only. |