[mira_talk] Re: Problems using sff extract
- From: Ganga Jeena <ganga.jeena@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 14 Dec 2010 17:50:44 +0530
[dc103@compute-0-0 orig_data]$ ~/apps/mira/bin/sff_extract -l
flx_linker.fa -i "insert_size:8000, insert_stdev:1000"
/home/dc103/CP_Data/sff_lf/GSMQLLJ01.sff >LOG&
[dc103@compute-0-0 orig_data]$ Working on
'/home/dc103/CP_Data/sff_lf/GSMQLLJ01.sff':
Creating temporary sequences from reads in
'/home/dc103/CP_Data/sff_lf/GSMQLLJ01.sff' ... done.
Searching linker sequences with SSAHA2 (this may take a while) ...
An error occured during the SSAHA2 execution, aborting.
On Tue, Dec 14, 2010 at 2:28 PM, Ganga Jeena <ganga.jeena@xxxxxxxxx> wrote:
> [dc103@hpc orig_data]$ which ssaha2
> /usr/local/bin/ssaha2
>
>
> [dc103@hpc orig_data]$ /usr/local/bin/ssaha2
>
>
> ========================
> = SSAHA2 version 2.5.3 =
> ========================
>
> by Hannes Ponstingl, Adam Spargo and Zemin Ning.
>
> Copyright (C) 2003-2010 The Wellcome Trust Sanger Institute, Cambridge, UK.
> All Rights Reserved.
>
> SSAHA2 is a package combining SSAHA with cross_match developed
> by Phil Green at the University of Washington.
>
> Reference: Ning Z, Cox AJ, Mullikin JC.
> SSAHA: a fast search method for large DNAdatabases.
> Genome Res. 2001 Oct;11(10):1725-9.
>
> DESCRIPTION:
>
> ssaha2Build This program constructs the hashtable
> required by the other ssaha2 programs.
> This provides an index for the given subject
> sequence.
>
> ssaha2 This program aligns query sequences against a
> subject hashtable.
>
> ssahaSNP ssahaSNP is a polymorphism detection tool.
> It detects homozygous SNPs and indels by aligning
> shotgun reads to the finished genome sequence.
> From the best alignment, SNP candidates are
> screened, taking into account the quality value
> of the bases with variation as well as the quality
> values in the neighbouring bases, using
> neighbourhood quality standard (NQS).
>
> USAGE:
> *************************************************************
> * NOTE: SSAHA2 & SSAHASNP COMMAND LINE FORMATS HAVE CHANGED *
> * with version 1.0.9 *
> *************************************************************
>
> ssaha2Build [OPTIONS] -save <hash name> <subject file>
>
> ssaha2 [OPTIONS] -save <hash name> <query file> [<query file 2nd>]
> ssaha2 [OPTIONS] <subject file> <query file> [<query file 2nd>]
>
> ssahaSNP [OPTIONS] -save <hash name> <query file>
> ssahaSNP [OPTIONS] <subject file> <query file>
>
> where <subject file> and <query file> are fasta or fastq files with
> the reference (subject) and query sequence files. <hash name> is
> the root name of the hash table files created from the reference
> sequence using ssaha2Build.
> The paired-end module invoked with the -pair option (see below)
> expects two query files with file <query file> containing the first
> and <query file 2nd> containing the second mate of each pair. The
> mates of a paired-end read must occur at the same postion in the
> sequence of reads in <query file> and <query file 2nd>. The paired-
> end module is not available for ssahaSNP.
>
> OPTIONS:
>
> -h, -help Print this page.
> -v, -version Print version information.
> -c, -cookbook Print some example parameter sets, suitable
> for common tasks.
>
> All other options, except the '-solexa' and '-454' flags and the
> '-output ssaha2 cigar' option, are key-value pairs. Options are described
> below
> (default values in brackets):
>
> -save <FILENAME>
> ssaha2Build: Root name of the files to which the
> hash table is saved. The set of files
> have the extensions FILENAME.head FILENAME.body
> FILENAME.name FILENAME.base FILENAME.size
> ssaha2, ssahaSNP: Read hash table from files created by
> ssaha2Build.
> If -save is not specified then the first file
> name
> specifies the reference sequence for which a hash
> table is constructed on the fly
>
> -kmer Word size for ssaha hashing (13).
>
> -skip Step size for ssaha hashing (13).
>
> -ckmer Word size for cross_match matching (10).
>
> -cmatch Minimum match length for cross_match matching (14).
>
> -cut Number of repeats allowed before this kmer is ignored (10000).
>
> -seeds Number of kmer matches required to flag a hit (5).
>
> -depth Number of hits to consider for alignment (50).
>
> -memory: Memory assigned in MBs for the alignment matrix (200).
>
> -score Minimum score for match to be reported (30).
>
> -identity Minimum identity (as percentage) for match to be reported
> (50.000000).
>
> -port Port number for server (60000).
>
> -align If set to > 0, output graphical alignment (0).
> If set to 2 and -solexa flag is set: output also quality score.
>
> -edge (obsolete as of release 2.0.0) Augment hit by this many bases
> before alignment (200).
>
> -array: Memory assigned in bytes for frequency arrays (4000000).
>
> -start: first sequence to process in query (0).
>
> -end: last sequence to process in query, 0 means process all (0).
>
> -sense (obsolete as of release 2.0.0) Allow really patchy hits to go
> for alignment (0).
>
> -best If set to 1, only report the best alignment for each
> match, if multiple best scores report all (65). If set to a
> negative value '-best -<b>' report alignment only if there are
> at most <b> best mappings.
>
> -454: (see -rtype) Tune for 454 reads (0). Implies '-skip 3 -seeds 2
> -score 30 -sense 1 -cmatch 10 -ckmer 6'
>
> -NQS: Use NQS to filter SNPs if set to 1, otherwise output all
> candidates (1).
>
> -quality: Quality value to use for variation base in NQS (23).
>
> -tags: If set to 1, prefix added to output summary lines to
> aid parsing, the prefix depends upon the chosen
> output format, e.g. if output is ssaha2 then the
> prefix is ALIGNMENT (1).
>
> -output: ssaha2 - original ssaha2 line only (default)
> sugar - Simple UnGapped Alignment Report
> cigar - Compact Idiosyncratic Gapped Alignment Report
> vulgar - Verbose Useful Labelled Gapped Alignment Report
> psl - Tab separated format similar to BLT
>
> http://genome.ucsc.edu/goldenPath/help/customTrack.html
> pslx - Tab separated format with sequence
> gff - http://www.sanger.ac.uk/Software/formats/GFF/
> ssaha2 cigar - alternate between ssaha2 and cigar format lines
> aln - Tony Cox' alignment output format.
> sam - SAM format (http://samtools.sourceforge.net).
> Output
> is written to a file specified with the -oufile
> flag.
>
> sam_soft - SAM format using soft clipping. The entire read
> is
> output./n/n for a full description of
> output formats see:
>
> http://www.sanger.ac.uk/Software/analysis/SSAHA2/formats.shtml
>
> -name Flag that modifies option '-output cigar' such that read name
> and length are also reported when there was no hit found.
>
> -diff: Output all hits within diff of the best (-1).
>
> -udiff: Ignore best hit if second best score within udiff (0).
>
> -fix: If set to 1, fix -edge, -seeds, -score so that they
> are not updated according to read length in ssahaSNP (0).
>
> -disk: 0: map all files into memory including the query sequences. (0)
> 1: read hashtable body, the subject and query sequences from
> disk
> rather than loading them into memory.
> 2: like 1 but the subject sequences are read into memory. The
> body
> is left on the disk.
> In both cases the query sequence file is not mapped into
> memory.
> -weight: If >0, apply this much weighting to rare kmers (0).
>
> -solexa: (see -rtype) implies (ssaha2 and ssahaSNP only):
> -kmer 13 -skip 2 -seeds 2 -score 12 -cmatch 9 -ckmer 6.
> Top scoring hits with lower quality at the mismatch positions
> have their Smith-Waterman score incremented by 1. Mapping
> scores are changed accordingly. SsahaSNP reports in such cases
> only the top scoring hit (no Repeat lines).
>
> -rtype: solexa - like -solexa flag
> 454 - like -454 flag
> abi - tunes for ABI reads (default)
>
> -pair <dist_lower>,<dist_upper>: Map paired-end reads with an insert
> length in
> the interval [<dist_lower>,<dist_upper>]. The reads for each
> mate
> are in a separate input file named by the last two tokens of
> the
> command line. The sequence for both mates are read in the same
> direction. Paired-end reads are reported if the mates match
> within
> <dist_upper> bases from each other, but at least <dist_lower>
> bases
> apart. No mate is reported, if the mapping is ambiguous, i.e.
> if
> there are multipe hits with the same Smith-Waterman alignment
> score
> in the specified distance range.
> If hits are found only for one mate, the highest scoring hit is
> reported for this mate unless it is ambiguous.
>
> -outfile <file_name> Output file for output in SAM format or, if the -pair
> option is set, for mate pairs that map outside the specified
> distance range unambiguously (each with a mapping score > 30,
> or a
> value set with the -mthresh option below).
>
> -mthresh <mapping_score> Threshold in the mapping score for mate pairs to
> be
> reported that map outside the distance range (see option
> -outfile).
> <mapping_score> is an integer between 0 and 50 (default: 30).
> This option requires the -pair option to be set.
>
> -multi <rand_seed> Flag modifying the way paired-end reads with multiple
> (repetitive) mappings are reported. If rand_seed == 0: skip
> such
> pairs entirely. if rand_seed> 0: select one pair at random.
> <rand_seed> seeds the random number generator.
>
>
>
>
> On Tue, Dec 14, 2010 at 2:17 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>
>> On Dienstag 14 Dezember 2010 Ganga Jeena wrote:
>> > [dc103@hpc orig_data]$ /usr/local/bin/sff_extract -o cp_454 -a -l
>> > flx_linker.fa -i "insert_size:8000, insert_stdev:1000"
>> > /home/dc103/CP_Data/sff_lf/GSMQLLJ01.sff
>> > [Errno 22] Invalid argument
>> >
>>
>> No, not
>>
>> /usr/local/bin/sff_extract
>>
>> but
>>
>> /usr/local/bin/ssaha2
>>
>> While we are at it: what does
>>
>> which ssaha2
>>
>> say?
>>
>> B.
>>
>> --
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>> visit http://www.chevreux.org/mira_mailinglists.html
>>
>
>
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