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Dear authors, I am encountering an issue while applying apply_scaling_factor with use.optimal.R = TRUE in ABEMUS. The error appears on most samples but not systematically. I manage to get the optimalR.tsv file for a few samples.

I get the following error:
in line 61 of apply_scaling_factor: tabindex[i,paste0("tabcalls_f3","_optimalR_used")] <- optR
Error in [<-.data.frame(*tmp*, i, paste0("tabcalls_f3", "_optimalR_used"), :
replacement has 2 rows, data has 1

This is due to the fact that I get 2 Ropt values instead of a single in those failing cases.
This looks like this is due to the fact tab_optimal_R has 2 entries for target_Mbp=4.40 and mean_coverage=200 (row ID 15 and 17). Why is that?

How to solve this issue?
Shall we remove this double option of scaling factor in tab_optimal_R?

Many thanks in advance for your help,
Kind regards,
Hanaé

tab_optimal_R
target_Mbp mean_coverage scalingfactor
6 0.04 200 1.1
7 0.04 500 1.1
8 0.04 1000 1.1
5 0.04 2000 1.1
10 0.20 200 1.2
11 0.20 500 1.1
12 0.20 1000 1.1
9 0.20 2000 1.2
18 0.40 200 1.2
19 0.40 500 1.1
20 0.40 1000 1.1
13 0.40 2000 1.2
26 1.10 200 1.2
27 1.10 500 1.1
28 1.10 1000 1.1
25 1.10 2000 1.2
34 2.10 200 1.2
35 2.10 500 1.1
36 2.10 1000 1.1
33 2.10 2000 1.1
15 4.40 200 1.4
17 4.40 200 1.2
16 4.40 500 1.1
14 4.40 2000 1.1
22 8.90 200 2.2
23 8.90 500 1.2
24 8.90 1000 1.3
21 8.90 2000 1.2
30 17.70 200 2.2
31 17.70 500 1.3
32 17.70 1000 1.4
29 17.70 2000 1.3
38 26.60 200 2.2
39 26.60 500 1.5
40 26.60 1000 1.4
37 26.60 2000 1.3
2 36.00 200 2.2
3 36.00 500 2.2
4 36.00 1000 1.4
1 36.00 2000 1.4

Please find below an example of the values of my variables used at this point of the function:

target_size
[1] 4.995

sizes
[1] 0.04 0.20 0.40 1.10 2.10 4.40 8.90 17.70 26.60 36.00

closest_target_size
[1] 4.4

bombanel
target_Mbp mean_coverage scalingfactor
15 4.4 200 1.4
17 4.4 200 1.2
16 4.4 500 1.1
14 4.4 2000 1.1

covs
[1] 200 200 500 2000

closest_coverage
[1] 200 200

optR
[1] 1.4 1.2

Hi there,
I am having issues in calling the "callsnvs" command. Error is:
Error in names(snvs) <- c("chr", "pos", "ref", "alt", "A", "C", "G", "T", : 'names' attribute [15] must be the same length as the vector [11]

I succeeded in all steps except this one. I write the commands I used here, so maybe someone can suggest a solution:

split_pacbam_bychrom(targetbed = args$regions, pacbamfolder = args$pacbamFolder, pacbamfolder_bychrom = args$pacbamByChromFolder)

perBaseErrorModel <- compute_pbem(sample.info.file = args$sampleInfo, targetbed = args$regions, outdir = args$outDir, pacbamfolder_bychrom = args$pacbamByChromFolder)

allelicFractionThresholds <- compute_afthreshold(outdir = args$outDir, pbem_dir = file.path(args$outDir,"BaseErrorModel"))

snvs <- callsnvs(sample.info.file = args$sampleInfo, controls_dir = file.path(args$outDir,"Controls"), pbem_dir = file.path(args$outDir,"BaseErrorModel"), detection.specificity = 0.995, replicas = 10, outdir = args$outDir, outdir.calls.name = "SNVs", targetbed = args$regions, pacbamfolder_bychrom = args$pacbamByChromFolder)`

Structure of folders is correct and so the generated files. Any idea?

Thanks!

Hello,
The function callsnvs threw this error:

Error in fread(input = tabpbem_file, stringsAsFactors = FALSE, showProgress = FALSE,  : 
 input= must be a single character string containing a file name, a system command containing at least one space, a URL starting 'http[s]://', 'ftp[s]://' or 'file://', or, the input data itself containing at least one \n or \r

The problem is caused by filter.R at line 108. Instead of
tabpbem_file = list.files(pbem_dir, pattern = paste0('bperr',chrom,'.tsv'),full.names = TRUE)
it should be
tabpbem_file = list.files(pbem_dir, pattern = paste0('bperr_chr',chrom,'.tsv'),full.names = TRUE)

The fix makes the function look for a file like bperr_chr1.tsv instead of bperr_1.tsv.

Kind regards,
Andrej
PS: I used hg38 as reference. I don't know how the files in outdir.bperr.name get named when using hg19.

Just working through test_example.R with R/4.0.2. Final steps to apply the pbem scaling factor to calls, doesn't output the optimalR tsv files? After calling the apply_scaling_factor(xxx) method, does one need to do something else? When heading the calls, e.g. head( calls$tabsnvs_index_scalfact ) the file paths are in the table but don't actually exist, see below. Any suggestions? Thanks

head( calls$tabsnvs_index_scalfact )
patient plasma germline
1 PT01 TUMOR_A CTRL_A
2 PT01 TUMOR_B CTRL_B
3 PT02 TUMOR_C CTRL_C
5 PT04 TUMOR_E
tabcalls_f1
1 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_A/pmtab_F1_TUMOR_A.tsv
2 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_B/pmtab_F1_TUMOR_B.tsv
3 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_C/pmtab_F1_TUMOR_C.tsv
5 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_E/pmtab_F1_TUMOR_E.tsv
tabcalls_f2
1 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_A/pmtab_F2_TUMOR_A.tsv
2 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_B/pmtab_F2_TUMOR_B.tsv
3 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_C/pmtab_F2_TUMOR_C.tsv
5 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_E/pmtab_F2_TUMOR_E.tsv
tabcalls_f3
1 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_A/pmtab_F3_TUMOR_A.tsv
2 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_B/pmtab_F3_TUMOR_B.tsv
3 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_C/pmtab_F3_TUMOR_C.tsv
5 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_E/pmtab_F3_TUMOR_E.tsv
case_mean_coverage
1 2286.657
2 2293.896
3 2285.669
5 2292.059
tabcalls_f3_optimalR
1 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_A/pmtab_F3_optimalR_TUMOR_A.tsv
2 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_B/pmtab_F3_optimalR_TUMOR_B.tsv
3 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_C/pmtab_F3_optimalR_TUMOR_C.tsv
5 /uufs/chpc.utah.edu/common/HIPAA/u0028003/Scratch/Underhill/Abemus/test_dataset_abemus//Results/TUMOR_E/pmtab_F3_optimalR_TUMOR_E.tsv
tabcalls_f3_optimalR_used
1 1.1
2 1.1
3 1.1
5 1.1