Near to finishing step, nextflow stop throwing this issue:
Warning message:
In DESeqDataSet(rse, design, ignoreRank = TRUE) :
some variables in design formula are characters, converting to factors
Fit for gene/exon ENSG00000140443 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000164509 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000213096+ENSG00000268362 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000242125+ENSG00000180198+ENSG00000274266 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000252481+ENSG00000247092 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000283268+ENSG00000133316+ENSG00000222328 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000054793 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000140443 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000156508 threw the next warning(s): Too much damping - convergence tolerance not achievable
Fit for gene/exon ENSG00000213096+ENSG00000268362 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000242125+ENSG00000180198+ENSG00000274266 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000282885+ENSG00000274012 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000242125+ENSG00000180198+ENSG00000274266 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000283268+ENSG00000133316+ENSG00000222328 threw the next warning(s): the matrix is either rank-deficient or indefinite
My run command was:
nextflow run nf-core/rnasplice --input samplesheet.csv --contrasts contrastsheet.csv --outdir nextflow_out -profile singularity --gtf Homo_sapiens.GRCh38.113.chr.gtf --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa --gene_bed Homo_sapiens.GRCh38.dna.primary_assembly.filtered.bed --transcript_fasta genome.transcripts.fa --aligner star_salmon --save_trimmed True --skip_markduplicates --skip_dupradar --star_index star --salmon_index salmon --rsem_index rsem --sashmi_plot True --miso_genes "ENSG00000000457.14,ENSG00000000971.17,ENSG00000005810.20" --max_cpu 10
Near to finishing step, nextflow stop throwing this issue:
Warning message:
In DESeqDataSet(rse, design, ignoreRank = TRUE) :
some variables in design formula are characters, converting to factors
Fit for gene/exon ENSG00000140443 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000164509 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000213096+ENSG00000268362 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000242125+ENSG00000180198+ENSG00000274266 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000252481+ENSG00000247092 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000283268+ENSG00000133316+ENSG00000222328 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000054793 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000140443 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000156508 threw the next warning(s): Too much damping - convergence tolerance not achievable
Fit for gene/exon ENSG00000213096+ENSG00000268362 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000242125+ENSG00000180198+ENSG00000274266 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000282885+ENSG00000274012 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000242125+ENSG00000180198+ENSG00000274266 threw the next warning(s): the matrix is either rank-deficient or indefinite
Fit for gene/exon ENSG00000283268+ENSG00000133316+ENSG00000222328 threw the next warning(s): the matrix is either rank-deficient or indefinite
My run command was:
nextflow run nf-core/rnasplice --input samplesheet.csv --contrasts contrastsheet.csv --outdir nextflow_out -profile singularity --gtf Homo_sapiens.GRCh38.113.chr.gtf --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa --gene_bed Homo_sapiens.GRCh38.dna.primary_assembly.filtered.bed --transcript_fasta genome.transcripts.fa --aligner star_salmon --save_trimmed True --skip_markduplicates --skip_dupradar --star_index star --salmon_index salmon --rsem_index rsem --sashmi_plot True --miso_genes "ENSG00000000457.14,ENSG00000000971.17,ENSG00000005810.20" --max_cpu 10