Hello Everyone,
I am currently analysing GBS data using stacks software as i ma currently facing some problem with ref_map.pl.
According to this script not getting proper output for this run.
this is the log file information form ref_map.pl
I am currently analysing GBS data using stacks software as i ma currently facing some problem with ref_map.pl.
According to this script not getting proper output for this run.
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ref_map.pl version 1.37 started at 2016-04-29 16:52:29 /usr/local/bin/ref_map.pl -T 4 -m 3 -n 1 -b 2 -o ref_out/ -S -s RG-1.bam Identifying unique stacks; file 1 of 1 [RG-1] /usr/local/bin/pstacks -t bam -f RG-1.bam -o ref_out -i 1 -p 4 -m 3 2>&1 Min depth of coverage to report a stack: 3 Model type: SNP Alpha significance level for model: 0.05 BAM support was not enabled when Stacks was compiled. Parsing RG-1.bam Analyzed 0 sequence reads; Identified 0 unique stacks from those reads. Merged 0 unique Stacks into 0 loci. Identifying polymorphic sites and calling consensus sequences...done. Number of utilized reads 0 Mean coverage depth is -nan; Std Dev: -0; Max: 0 Writing loci, SNPs, alleles to 'ref_out/...' Wrote 0 loci, excluded 0 loci due to insuffient depth of coverage; blacklisted 0 loci. /usr/local/bin/cstacks -g -b 2 -o ref_out -s ref_out/RG-1 -p 4 -n 1 2>&1 Number of mismatches allowed between stacks: 1 Loci matched based on genomic location. Constructing catalog from 1 samples. Initializing new catalog... Parsing ref_out/RG-1.tags.tsv.gz Parsing ref_out/RG-1.snps.tsv.gz Parsing ref_out/RG-1.alleles.tsv.gz Building an index of the catalog. Writing catalog to 'ref_out/... done. /usr/local/bin/sstacks -g -b 2 -c ref_out/batch_2 -o ref_out -s ref_out/RG-1 -p 4 2>&1 Searching for matches by genomic location... Parsing ref_out/batch_2.catalog.tags.tsv.gz Parsing ref_out/batch_2.catalog.snps.tsv.gz Parsing ref_out/batch_2.catalog.alleles.tsv.gz Processing sample 'ref_out/RG-1' [1 of 1] Parsing ref_out/RG-1.tags.tsv.gz Parsing ref_out/RG-1.snps.tsv.gz Parsing ref_out/RG-1.alleles.tsv.gz /usr/local/bin/populations -b 2 -P ref_out -s -t 4 2>&1 A population map was not specified, all samples will be read from 'ref_out/' as a single popultaion. Fst kernel smoothing: off Bootstrap resampling: off Percent samples limit per population: 0 Locus Population limit: 1 Minimum stack depth: 0 Log liklihood filtering: off; threshold: 0 Minor allele frequency cutoff: 0 Maximum observed heterozygosity cutoff: 1 Applying Fst correction: none. No population map specified, building file list. Found 2 input file(s). 1 population found 1: RG-1, RG-1.sorted 1 group of populations found 1: 1 Parsing ref_out/batch_2.catalog.tags.tsv.gz Parsing ref_out/batch_2.catalog.snps.tsv.gz Parsing ref_out/batch_2.catalog.alleles.tsv.gz Catalog is not reference aligned, arbitrarily ordering catalog loci. Unable to open 'ref_out/RG-1' Warning: unable to find any matches in file 'RG-1', excluding this sample from population analysis. Unable to open 'ref_out/RG-1.sorted' Warning: unable to find any matches in file 'RG-1.sorted', excluding this sample from population analysis. Populating observed haplotypes for 0 samples, 0 loci. Writing SQL markers file to 'ref_out/batch_2.markers.tsv' Removing 0 loci that did not pass sample/population constraints... retained 0 loci. refmap_map.pl completed at 2016-04-29 16:52:29
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