I am using Tassel 3 command pipeline to analyze the GBS data to get SNP from a population, and have the similar problem on "TagsToSNPByAlignmentPlugin". This plugin of the pipeline is not stable.
The log says parameters are wrong and -i option file is not found. Actually the file is there. I tested this using command as below:
#the output shows the file in there. pasted in the following line.
rw-r--r-- 1 wangxuewen users 525220792 2014-05-01 00:18 mergedTBT/myStudyp1.tbt.byte
I also paste the full log file containing the details below. Has anyone have good suggestion on how to resolve the problem? Does anyone know how to use the graphic interface to do GBS SNP analyzing?
Thanks.
The following is the error message : [main] ERROR net.maizegenetics.pipeline.
TasselPipeline - java.lang.IllegalArgumentException: Can't find the TagsByTaxa input file (-i option: mergedTBT/myStudyp1.tbt.byte).
Tassel
Pipeline Arguments: -fork1 -TagsToSNPByAlignmentPlugin -y -i
mergedTBT/myStudyp1.tbt.byte -m topm/myMasterTags.topm -mUpd
topm/myMasterTagsWithVariants.
topm -o h
apmap/raw/myGBSGenos_chr+.hmp.txt -mnF 0.8 -p myPedigreeFile.ped -ref refseq -mnMAF 0.01 -mnMAC 100000 -sC 1 -eC 212441 -endPlugin -runfork1
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 3.0.164 Date: December 5, 2013
INFO -
The available options for the TagsToSNPByAlignmentPlugin are as follows:
-i Input .tbt file
-y Use byte-formatted TBT file (*.tbt.byte)
-m TagsOnPhysicalMap file containing genomic position of tags
-mUpd Update TagsOnPhysicalMap file with allele calls, saved to specified file
-o Output HapMap file. Use a plus sign (+) as a wild card character in place of the chromosome number
(e.g., ./hapmap/raw/myGBSGenos_chr+.hmp.txt)
-mxSites Maximum number of sites (SNPs) output per chromosome (default: 200000)
-mnF Minimum F (inbreeding coefficient) (default: -2.0 = no filter)
-p Pedigree file containing full sample names (or expected names after merging) & expected inbreeding
coefficient (F) for each. Only taxa with expected F >= mnF used to calculate F = 1-Ho/He.
(default: use ALL taxa to calculate F)
-mnMAF Minimum minor allele frequency (default: 0.01)
-mnMAC Minimum minor allele count (default: 10)
-mnLCov Minimum locus coverage (proportion of Taxa with a genotype) (default: 0.1)
-errRate Average sequencing error rate per base (used to decide between heterozygous and homozygous calls) (default: 0.01)
-ref Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included
when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site
is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon).
DEFAULT: Don't use reference genome.
-inclRare Include the rare alleles at site (3 or 4th states) (default: false)
-inclGaps Include sites where major or minor allele is a GAP (default: false)
-sC Start chromosome
-eC End chromosome
[main] INFO net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin -
The available options for the TagsToSNPByAlignmentPlugin are as follows:
-i Input .tbt file
-y Use byte-formatted TBT file (*.tbt.byte)
-m TagsOnPhysicalMap file containing genomic position of tags
-mUpd Update TagsOnPhysicalMap file with allele calls, saved to specified file
-o Output HapMap file. Use a plus sign (+) as a wild card character in place of the chromosome number
(e.g., ./hapmap/raw/myGBSGenos_chr+.hmp.txt)
-mxSites Maximum number of sites (SNPs) output per chromosome (default: 200000)
-mnF Minimum F (inbreeding coefficient) (default: -2.0 = no filter)
-p Pedigree file containing full sample names (or expected names after merging) & expected inbreeding
coefficient (F) for each. Only taxa with expected F >= mnF used to calculate F = 1-Ho/He.
(default: use ALL taxa to calculate F)
-mnMAF Minimum minor allele frequency (default: 0.01)
-mnMAC Minimum minor allele count (default: 10)
-mnLCov Minimum locus coverage (proportion of Taxa with a genotype) (default: 0.1)
-errRate Average sequencing error rate per base (used to decide between heterozygous and homozygous calls) (default: 0.01)
-ref Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included
when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site
is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon).
DEFAULT: Don't use reference genome.
-inclRare Include the rare alleles at site (3 or 4th states) (default: false)
-inclGaps Include sites where major or minor allele is a GAP (default: false)
-callBiSNPsWGap Include sites where the third allele is a GAP (default: false)
-sC Start chromosome
-eC End chromosome
[main] ERROR net.maizegenetics.pipeline.TasselPipeline - java.lang.IllegalArgumentException: Can't find the TagsByTaxa input file (-i option: mergedTBT/
myStudyp1.tbt.by
te).
java.lang.IllegalArgumentException: TasselPipeline: parseArgs: Unknown parameter: -TagsToSNPByAlignmentPlugin
at net.maizegenetics.pipeline.TasselPipeline.parseArgs(TasselPipeline.java:1233)
at net.maizegenetics.pipeline.TasselPipeline.<init>(TasselPipeline.java:121)
at net.maizegenetics.pipeline.TasselPipeline.main(TasselPipeline.java:161)