Open thebrownlife opened 4 months ago
dariober
commented
4 months ago 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
commented
4 months ago 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
commented
1 month ago Hi,
I have the same error message. Have you found a solution?
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 recordsCan someone please explain the chromosomes have unknown reference name? Thank you!