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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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Duplicate levels error after loading GenomeInfoD using mouse reference #102

Closed mheskett closed 3 years ago

mheskett commented 3 years ago

Hi there. I have followed all the instructions to create the mouse reference files with HMMCopy and now run into this error using low pass WGS of mouse tumors. Any help on how I can troubleshoot this, or if it is a bug please let me know.

Thanks! Here is the call:

Rscript /home/groups/Spellmandata/heskett/packages/envs/chris.ichor/share/r-ichorcna-0.1.0.20180710-0/scripts/runIchorCNA.R --id $filename \ --WIG $sample_wig --gcWig ../mm10.reference/refdata-gex-mm10-2020-A/fasta/genome.gc.wig \ --mapWig ../mm10.reference/refdata-gex-mm10-2020-A/fasta/genome2.50000.window.wig \ --ploidy "c(2)" --normal "c(0.9)" --maxCN 8 --includeHOMD False --estimateNormal True --estimatePloidy True \ --estimateScPrevalence True \ --txnE 0.9999 --txnStrength 10000 --fracReadsInChrYForMale 0.001 --plotFileType png --plotYLim "c(-2,4)" --outDir $out_dir

See below for the errors

Loading tumour file:405G.sorted.markdup.bam Slurping: ../alignments/405G.sorted.markdup.bam.wig Parsing: fixedStep chrom=chr1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr2 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr3 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr4 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr5 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr6 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr7 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr8 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr9 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr10 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr11 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr12 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr13 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr14 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr15 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr16 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr17 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr18 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr19 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chrX start=1 step=50000 span=50000 Parsing: fixedStep chrom=chrY start=1 step=50000 span=50000 Sorting by decreasing chromosome size Reading GC and mappability files Slurping: ../mm10.reference/refdata-gex-mm10-2020-A/fasta/genome.gc.wig Parsing: fixedStep chrom=chr1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr10 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr11 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr12 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr13 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr14 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr15 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr16 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr17 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr18 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr19 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr2 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr3 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr4 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr5 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr6 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr7 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr8 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr9 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chrM start=1 step=16299 span=16299 Parsing: fixedStep chrom=chrX start=1 step=50000 span=50000 Parsing: fixedStep chrom=chrY start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584299.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456233.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584301.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456211.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456350.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584293.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456221.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584297.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584296.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456354.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584294.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584298.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584300.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456219.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456210.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584303.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584302.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456212.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584304.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456379.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456216.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456393.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456366.1 start=1 step=47073 span=47073 Parsing: fixedStep chrom=GL456367.1 start=1 step=42057 span=42057 Parsing: fixedStep chrom=GL456239.1 start=1 step=40056 span=40056 Parsing: fixedStep chrom=GL456213.1 start=1 step=39340 span=39340 Parsing: fixedStep chrom=GL456383.1 start=1 step=38659 span=38659 Parsing: fixedStep chrom=GL456385.1 start=1 step=35240 span=35240 Parsing: fixedStep chrom=GL456360.1 start=1 step=31704 span=31704 Parsing: fixedStep chrom=GL456378.1 start=1 step=31602 span=31602 Parsing: fixedStep chrom=GL456389.1 start=1 step=28772 span=28772 Parsing: fixedStep chrom=GL456372.1 start=1 step=28664 span=28664 Parsing: fixedStep chrom=GL456370.1 start=1 step=26764 span=26764 Parsing: fixedStep chrom=GL456381.1 start=1 step=25871 span=25871 Parsing: fixedStep chrom=GL456387.1 start=1 step=24685 span=24685 Parsing: fixedStep chrom=GL456390.1 start=1 step=24668 span=24668 Parsing: fixedStep chrom=GL456394.1 start=1 step=24323 span=24323 Parsing: fixedStep chrom=GL456392.1 start=1 step=23629 span=23629 Parsing: fixedStep chrom=GL456382.1 start=1 step=23158 span=23158 Parsing: fixedStep chrom=GL456359.1 start=1 step=22974 span=22974 Parsing: fixedStep chrom=GL456396.1 start=1 step=21240 span=21240 Parsing: fixedStep chrom=GL456368.1 start=1 step=20208 span=20208 Parsing: fixedStep chrom=JH584292.1 start=1 step=14945 span=14945 Parsing: fixedStep chrom=JH584295.1 start=1 step=1976 span=1976 Sorting by decreasing chromosome size Slurping: ../mm10.reference/refdata-gex-mm10-2020-A/fasta/genome2.50000.window.wig Parsing: fixedStep chrom=GL456210.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456211.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456212.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456213.1 start=1 step=39340 span=39340 Parsing: fixedStep chrom=GL456216.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456219.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456221.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456233.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456239.1 start=1 step=40056 span=40056 Parsing: fixedStep chrom=GL456350.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456354.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456359.1 start=1 step=22974 span=22974 Parsing: fixedStep chrom=GL456360.1 start=1 step=31704 span=31704 Parsing: fixedStep chrom=GL456366.1 start=1 step=47073 span=47073 Parsing: fixedStep chrom=GL456367.1 start=1 step=42057 span=42057 Parsing: fixedStep chrom=GL456368.1 start=1 step=20208 span=20208 Parsing: fixedStep chrom=GL456370.1 start=1 step=26764 span=26764 Parsing: fixedStep chrom=GL456372.1 start=1 step=28664 span=28664 Parsing: fixedStep chrom=GL456378.1 start=1 step=31602 span=31602 Parsing: fixedStep chrom=GL456379.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456381.1 start=1 step=25871 span=25871 Parsing: fixedStep chrom=GL456382.1 start=1 step=23158 span=23158 Parsing: fixedStep chrom=GL456383.1 start=1 step=38659 span=38659 Parsing: fixedStep chrom=GL456385.1 start=1 step=35240 span=35240 Parsing: fixedStep chrom=GL456387.1 start=1 step=24685 span=24685 Parsing: fixedStep chrom=GL456389.1 start=1 step=28772 span=28772 Parsing: fixedStep chrom=GL456390.1 start=1 step=24668 span=24668 Parsing: fixedStep chrom=GL456392.1 start=1 step=23629 span=23629 Parsing: fixedStep chrom=GL456393.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=GL456394.1 start=1 step=24323 span=24323 Parsing: fixedStep chrom=GL456396.1 start=1 step=21240 span=21240 Parsing: fixedStep chrom=JH584292.1 start=1 step=14945 span=14945 Parsing: fixedStep chrom=JH584293.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584294.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584295.1 start=1 step=1976 span=1976 Parsing: fixedStep chrom=JH584296.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584297.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584298.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584299.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584300.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584301.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584302.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584303.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=JH584304.1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr10 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr11 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr12 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr13 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr14 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr15 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr16 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr17 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr18 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr19 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr2 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr3 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr4 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr5 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr6 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr7 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr8 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr9 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chrM start=1 step=16299 span=16299 Parsing: fixedStep chrom=chrX start=1 step=50000 span=50000 Parsing: fixedStep chrom=chrY start=1 step=50000 span=50000 Sorting by decreasing chromosome size Correcting Tumour Loading required package: GenomeInfoDb Error inlevels<-(tmp, value = if (nl == nL) as.character(labels) else paste0(labels, : factor level [24] is duplicated Calls: loadReadCountsFromWig ... .as.data.frame.IntegerRangesList -> data.frame -> factor Execution halted

mheskett commented 3 years ago

trying to use the --buildGenome mm10 option with the recent version of ichor