Warning message: region "1" specifies an unknown reference name. Continue anyway.

[thebrownlife]

I have the bam files of a tumour sample "T11QM0022" and its matched normal sample "B11QM0022". They were generated using the GATK4 Best Practices pipeline. They are sorted and index. However, when I run the cnv_facets command on these bam files, I get the following messages on my Linux terminal.

[main_samview] region "1" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "1" specifies an unknown reference name. Continue anyway. Finished in 1.590000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "2" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "2" specifies an unknown reference name. Continue anyway. Finished in 1.680000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "3" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "3" specifies an unknown reference name. Continue anyway. Finished in 1.640000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "4" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "4" specifies an unknown reference name. Continue anyway. Finished in 1.530000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "5" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "5" specifies an unknown reference name. Continue anyway. Finished in 1.430000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "6" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "6" specifies an unknown reference name. Continue anyway. Finished in 1.400000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "7" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "7" specifies an unknown reference name. Continue anyway. Finished in 1.310000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "8" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "8" specifies an unknown reference name. Continue anyway. Finished in 1.310000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "9" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "9" specifies an unknown reference name. Continue anyway. Finished in 0.990000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "10" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "10" specifies an unknown reference name. Continue anyway. Finished in 1.130000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "11" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "11" specifies an unknown reference name. Continue anyway. Finished in 1.140000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "12" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "12" specifies an unknown reference name. Continue anyway. Finished in 1.090000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "13" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "13" specifies an unknown reference name. Continue anyway. Finished in 0.900000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "14" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "14" specifies an unknown reference name. Continue anyway. Finished in 0.750000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "15" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "15" specifies an unknown reference name. Continue anyway. Finished in 0.770000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "16" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "16" specifies an unknown reference name. Continue anyway. Finished in 0.880000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "17" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "17" specifies an unknown reference name. Continue anyway. Finished in 0.680000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "18" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "18" specifies an unknown reference name. Continue anyway. Finished in 0.880000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "19" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "19" specifies an unknown reference name. Continue anyway. Finished in 0.570000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "20" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "20" specifies an unknown reference name. Continue anyway. Finished in 0.500000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "21" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "21" specifies an unknown reference name. Continue anyway. Finished in 0.380000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "22" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "22" specifies an unknown reference name. Continue anyway. Finished in 0.350000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "X" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "X" specifies an unknown reference name. Continue anyway. Finished in 0.970000 seconds. [W::hts_idx_load2] The index file is older than the data file: B11QM0022.recal.bai [main_samview] region "Y" specifies an unknown reference name. Continue anyway. [W::hts_idx_load2] The index file is older than the data file: T11QM0022.recal.bai [main_samview] region "Y" specifies an unknown reference name. Continue anyway. Finished in 0.020000 seconds. [2024-04-16 16:28:22] Loading file T11QM0022.csv.gz... [2024-04-16 16:28:23] Analysis stopped: pileup file T11QM0022.csv.gz has no records

Can someone please explain the chromosomes have unknown reference name? Thank you!

[dariober]

The index file is older than the data file

Can you make sure the indexes are up-to-date with the bam files? In doubt, you can recreate them with:

samtools index tumor.bam
samtools index normal.bam

[thebrownlife]

Hi Dario, Thanks for your suggestion. I reindexed the bam files but the same error of "region "1" specifies an unknown reference name. Continue anyway." is still showing up. Any idea what may be causing it?

[JuleBrenningmeyer]

Hi,

I have the same error message. Have you found a solution?

[ankashchenko]

Hello! I faced with this problem when I used .vcf file with common SNPs from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/ as was recommended here https://github.com/mskcc/facets/issues/66. Chromosomes are labeled only by their number in this vcf file (1, 2, etc in CHROM column), whereas in my .bam files the labeling is chr1, chr2, etc. Therefore I got such error.

I simply used bcftools and additional .txt file to rename chromosomes in vcf: bcftools annotate --rename-chrs names.txt input.vcf.gz -O z -o output.vcf.gz

You can manually create names.txt. The example of such file: 1 chr1 2 chr2 3 chr3 4 chr4 5 chr5 6 chr6

After renaming I did not get this error anymore. So, just in case, check the labeling in your .bam and .vcf