{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/ichorCNA/issues/40","repository_url":"https://api.github.com/repos/broadinstitute/ichorCNA","labels_url":"https://api.github.com/repos/broadinstitute/ichorCNA/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/ichorCNA/issues/40/comments","events_url":"https://api.github.com/repos/broadinstitute/ichorCNA/issues/40/events","html_url":"https://github.com/broadinstitute/ichorCNA/issues/40","id":355794429,"node_id":"MDU6SXNzdWUzNTU3OTQ0Mjk=","number":40,"title":"Error when generating PoN","user":{"login":"andreykoch","id":10580169,"node_id":"MDQ6VXNlcjEwNTgwMTY5","avatar_url":"https://avatars3.githubusercontent.com/u/10580169?v=4","gravatar_id":"","url":"https://api.github.com/users/andreykoch","html_url":"https://github.com/andreykoch","followers_url":"https://api.github.com/users/andreykoch/followers","following_url":"https://api.github.com/users/andreykoch/following{/other_user}","gists_url":"https://api.github.com/users/andreykoch/gists{/gist_id}","starred_url":"https://api.github.com/users/andreykoch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andreykoch/subscriptions","organizations_url":"https://api.github.com/users/andreykoch/orgs","repos_url":"https://api.github.com/users/andreykoch/repos","events_url":"https://api.github.com/users/andreykoch/events{/privacy}","received_events_url":"https://api.github.com/users/andreykoch/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-30T23:57:55Z","updated_at":"2018-09-04T16:27:39Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nWhile trying to generate PoN, I'm getting an error.\r\n\r\n**I have previously generated 4 normal wig files using:**\r\n\r\n$readCounter --window 50000 --quality 20 --chromosome \"chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY\" $normal_sample.bam > $normal_sample.wig\r\n\r\n**Wig files have correct format:**\r\n\r\nfixedStep chrom=chr1 start=1 step=50000 span=50000\r\n5\r\n47\r\n31\r\n\r\n**The actual command line for the PoN generation:**\r\n\r\nRscript /rdseqdata/bin/ichorCNA-master/scripts/createPanelOfNormals.R \r\n--filelist /rndhome/akoch/SamBam_file_example/TMP/ref/wigPoNfiles.txt \r\n--gcWig /rdseqdata/bin/ichorCNA-master/inst/extdata/gc_hg19_50kb.wig \r\n--mapWig /rdseqdata/bin/ichorCNA-master/inst/extdata/map_hg19_50kb.wig \r\n--centromere /rdseqdata/bin/ichorCNA-master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt \r\n--outfile /rdseqdata/bin/ichorCNA-master/inst/extdata/PoN_hg19_50Kb_median_normAutosome_median.rds\r\n\r\n**The output before blowup:**\r\n\r\nLoading normal file:/rndhome/akoch/SamBam_file_example/TMP/ref/1801100551-NIK-3-26_TCATCTCC_L003_R1_export.wig\r\nSlurping: /rndhome/akoch/SamBam_file_example/TMP/ref/1801100551-NIK-3-26_TCATCTCC_L003_R1_export.wig\r\nParsing: fixedStep chrom=chr1 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr2 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr3 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr4 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr5 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr6 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr7 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr8 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr9 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr10 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr11 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr12 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr13 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr14 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr15 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr16 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr17 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr18 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr19 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr20 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr21 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chr22 start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chrX start=1 step=50000 span=50000\r\nParsing: fixedStep chrom=chrY start=1 step=50000 span=50000\r\nSorting by decreasing chromosome size\r\nReading GC and mappability files\r\nSlurping: /rdseqdata/bin/ichorCNA-master/inst/extdata/gc_hg19_50kb.wig\r\nParsing: fixedStep chrom=1 start=1 step=50000 span=50000\r\nError in seq.default(from = as.integer(tokens[2]), by = as.integer(tokens[3]), :\r\n'from' must be a finite number\r\nCalls: wigToRangedData -> seq -> seq.default\r\nExecution halted\r\n\r\n**Any help is greatly appreciated!**\r\n\r\nAndrey"},"comment":{"url":"https://api.github.com/repos/broadinstitute/ichorCNA/issues/comments/418432759","html_url":"https://github.com/broadinstitute/ichorCNA/issues/40#issuecomment-418432759","issue_url":"https://api.github.com/repos/broadinstitute/ichorCNA/issues/40","id":418432759,"node_id":"MDEyOklzc3VlQ29tbWVudDQxODQzMjc1OQ==","user":{"login":"gavinha","id":9221688,"node_id":"MDQ6VXNlcjkyMjE2ODg=","avatar_url":"https://avatars1.githubusercontent.com/u/9221688?v=4","gravatar_id":"","url":"https://api.github.com/users/gavinha","html_url":"https://github.com/gavinha","followers_url":"https://api.github.com/users/gavinha/followers","following_url":"https://api.github.com/users/gavinha/following{/other_user}","gists_url":"https://api.github.com/users/gavinha/gists{/gist_id}","starred_url":"https://api.github.com/users/gavinha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gavinha/subscriptions","organizations_url":"https://api.github.com/users/gavinha/orgs","repos_url":"https://api.github.com/users/gavinha/repos","events_url":"https://api.github.com/users/gavinha/events{/privacy}","received_events_url":"https://api.github.com/users/gavinha/received_events","type":"User","site_admin":false},"created_at":"2018-09-04T16:27:39Z","updated_at":"2018-09-04T16:27:39Z","author_association":"COLLABORATOR","body":"Hi @andreykoch \r\n\r\nThis is most likely due to the chromosome naming convention of the gc and map wig files.  Your normal samples have UCSC (\"chr\") chromosome names while the `gc_hg19_50kb.wig` and `map_hg19_50kb.wig` provided in the `inst/extdata/` directory uses NCBI (no \"chr\") convention.\r\n\r\nThere are 2 ways to solve this:\r\n1) You can duplicate the `gc_hg19_50kb.wig` and `map_hg19_50kb.wig` files and change chromosome names to use UCSC format. There are only 24 lines to change.\r\n2) We can improve the PoN creation script to handle this more directly.  The `runichorCNA.R` script does this but we have not had the change to update the PoN creation script.\r\n\r\nHope this helps.\r\n\r\nBest,\r\nGavin"}}
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