Closed DolapoA closed 1 month ago
Hello something went wrong in the generation of the ratio.txt aq you suggested with the "Inf" values. In the beginning of the output from the first command I see these two messages, on indicating that the pathway to the BAM file is not recognize properly and the second that the BAM has an EOF marker absent and that the bam is probably truncated.
Warning message:
In normalizePath(path_to_bam_file) :
path[1]="Alignments/sample1.sort.filtered": No such file or directory
"HRD/sample1/shallowHRD/sample1.sort.filtered.bam"
sample1.sort.filtered (1 of 1): extracting reads ...[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 byte
Something is wrong with your BAM file and probably how you indicated the filenames and how you generate your BAM. Align on hg19, only on the chromosomes 1-22, name your BAM file with an extension ".bam" at the end, you don't have it on the "sample1.sort.filtered" as it should and this will create an potential error.
Rscript QDNAseq_from_bam_no_chrX.R sample1.sort.filtered HRD/sample1/shallowHRD 50
Good luck keep me posted.
Alexandre
Hi Alexandre, Thanks, I will take a further look. I did get some results in my other samples with the same format but I will look at whether I can generate them successfully if I try again and make sure all paths are correct. Dolapo.
Thanks Alexandre, I've resolved the issue. I needed to generate my BAMs again! I appreciate your quick response. Looking forward to shallowHRD_v2!
All the best. Dolapo.
Hello Dolapo,
Good to know !!
Good luck on your research! Alexandre Eeckhoutte
Hello Alexandre,
I think that the issue is related to the ratio.txt result from QDNAseq having a many "Inf" entries.
I think the error bears some resemblance to a closed issue, namely: https://github.com/aeeckhou/shallowHRD/issues/15
Snippet of ratio.txt file "chromosome" "start" "ratio" "ratio_median"
Commands I have used:
Rscript QDNAseq_from_bam_no_chrX.R sample1.sort.filtered HRD/sample1/shallowHRD 50
Rscript shallowHRD_hg19_1.13_QDNAseq_no_chrX.R sample1.sort.filtered.bam_ratio.txt HRD/sample1/shallowHRD/ cytoband_adapted_hg19.csv
The log and error observed:
... x176 lines in total of -> Error: object 'THR' not found
Is there anything you could suggest for me to resolve this? For example would you recommend a different bin size during QDNAseq?