alleleFrequencies_chr1.txt is empty, rest are fine

[ronkesm]

Hi,

I am having a slightly strange issue with Battenberg. I am using the "_chr" hg38 reference files. The allelecounter step completes fine but leaves the [sample]_alleleFrequencies_chr1.txt file empty, so I end up with this error:

Error in read.table(paste0(TUMOURNAME, "_alleleFrequencies_chr", chr, : no lines available in input Calls: <Anonymous> ... prepare_wgs_cell_line -> cell_line_baf_logR -> read.table Execution halted

All other [sample]_alleleFrequencies_chr*.txt files are fine.

This is what my impute_info.txt file looks like:

1 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr1_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr1_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr1_impute.hap.gz 0 250000000 1 2 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr2_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr2_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr2_impute.hap.gz 0 245000000 1 3 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr3_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr3_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr3_impute.hap.gz 0 200000000 1 4 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr4_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr4_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr4_impute.hap.gz 0 195000000 1 5 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr5_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr5_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr5_impute.hap.gz 0 185000000 1 6 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr6_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr6_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr6_impute.hap.gz 0 175000000 1 7 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr7_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr7_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr7_impute.hap.gz 0 160000000 1 8 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr8_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr8_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr8_impute.hap.gz 0 150000000 1 9 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr9_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr9_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr9_impute.hap.gz 0 145000000 1 10 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr10_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr10_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr10_impute.hap.gz 0 140000000 1 11 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr11_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr11_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr11_impute.hap.gz 0 135000000 1 12 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr12_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr12_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr12_impute.hap.gz 0 135000000 1 13 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr13_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr13_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr13_impute.hap.gz 0 115000000 1 14 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr14_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr14_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr14_impute.hap.gz 0 110000000 1 15 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr15_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr15_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr15_impute.hap.gz 0 105000000 1 16 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr16_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr16_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr16_impute.hap.gz 0 90000000 1 17 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr17_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr17_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr17_impute.hap.gz 0 80000000 1 18 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr18_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr18_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr18_impute.hap.gz 0 80000000 1 19 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr19_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr19_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr19_impute.hap.gz 0 65000000 1 20 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr20_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr20_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr20_impute.hap.gz 20000000 65000000 1 21 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr21_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr21_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr21_impute.hap.gz 0 50000000 1 22 /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr22_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chr22_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chr22_impute.hap.gz 0 50000000 1 X /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chrX_PAR1_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chrX_PAR1_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chrX_PAR1_impute.hap.gz 0 2700000 1 X /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chrX_nonPAR_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chrX_nonPAR_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chrX_nonPAR_impute.hap.gz 2600000 155000000 0 X /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chrX_PAR2_impute.legend /data/globus/WGS/REF/battenberg/impute/genetic_map_chrX_PAR2_combined_b37.txt /data/globus/WGS/REF/battenberg/impute/ALL_1000G_phase1integrated_v3_chrX_PAR2_impute.hap.gz 154000000 156000000 1

I removed the 'chr' prefix from each entry in the impute_info.txt file as I would otherwise get this error:

sed: can't read PD48033a_alleleFrequencies_chr*.txt: No such file or directory Error in file(file, "rt") : cannot open the connection Calls: <Anonymous> ... prepare_wgs_cell_line -> cell_line_baf_logR -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'PD48033a_alleleFrequencies_chrchr1.txt': No such file or directory

As the script was reading the chromosome name from the impute_info.txt file 'chr1' and adding the 'chr' prefix to it.

I have also tried to run the scripts with the regular non "_chr" reference files and that fails immediately

[jcesar101]

Hi,

could you please provide the script used to launch this execution of Battenberg, and also, what version (tag or branch) are you currently using?

Thank you.