Somatic copy number analysis using WGS paired end wholegenome sequencing
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Error "No such file or directory) Error parsing loci file line" when run ascat.pl #120
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yufanzhouonline opened 3 weeks ago
Hi keiranmraine,
When run ascat.pl on Docker, I found an error.
Then I change SNP corrections files of chromosome 1, 2, 3 ... to chr1, chr2, chr3 to make chromosome labels same as bam file.
But the error is still there in "Sanger_CGP_Ascat_Implement_allele_count.1.err"
I only test chromosome 19 with command line:
ascat.pl -t /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_tumor_S26.rg.dup.sort.realn.chr19.bam -n /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_tail_S25.rg.dup.sort.realn.chr19.bam -r /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/mm10_selected.fa -sg /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/SnpGcCorrectionsYZnew.tsv -pr WGS -g XY -gc Y -o /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/changexy/ 2>&1 | tee runascat.log
The following is Sanger_CGP_Ascat_Implement_allele_count.1.err:
Would you please let me know how I fix this issue?
Thank you so much