ChrisHIV
commented
8 years ago Hi Olli, The --window-coords option means the windows you specify are interpreted with respect to the alignment of refs (found in RefsAln.fasta). Those coordinates are translated with respect to each individual ref, and it's those coordinates you see in the warning messages. Looks like your first window is to the left of the left-most edge of all of your bam references, because the coordinate translation gives 1-1 with respect to each of the bam references (presumably because in your external reference alignment file, one of them has more left-hand-side LTR than any of your bam references). Either choose your windows starting more to the right, by inspecting the aligned reference file (or even running FindInformativeWindows.py on it from the command line - just a one-liner), or use the pairwise option (probably easier). For the latter, note that the clinical genome starts at around position 800 for the HXB2 sequence you're using (so if you specify pairwise coordinate windows in 1-800 you'll be getting LTR reads which is probably not helpful).
olli0601
Hi Chris, I call
phylotypes.py 1 2 "ptyr1_bam.txt" "ptyr1_ref.txt" -Q1 24 -Q2 2 -P --window-coords 1,100,101,200,201,300,301,400,401,500,501,600,601,700,701,800,801,900,901,1000,1001,1100,1101,1200,1201,1300,1301,1400,1401,1500,1501,1600,1601,1700,1701,1800,1801,1900,1901,2000 --alignment-of-other-refs /Users/Oliver/Library/R/3.1/library/phyloscan/HIV1_compendium_AD_B_CPX.fasta --ref-for-rooting REF_CPX_AF460972_read_1_count_0 -T --x-raxml raxml --x-mafft mafft
and get the following warnings even though there seem to be long enough reads in the bam files:
Now processing window 601-700 Warning: bam file 15038_1_53 has no reads in window 1-1 Warning: bam file 15038_1_56 has no reads in window 1-1 Warning: bam file 15081_1_71 has no reads in window 1-1 Warning: bam file 15103_1_78 has no reads in window 1-1 Warning: bam file 15105_1_15 has no reads in window 1-1 Warning: bam file 15114_1_82 has no reads in window 1-1 Warning: bam file 15676_1_5 has no reads in window 1-1 Warning: bam file 15745_1_51 has no reads in window 1-1 Warning: bam file 15757_1_1 has no reads in window 1-1 Warning: bam file 15759_1_43 has no reads in window 1-1 Warning: bam file 15777_1_11 has no reads in window 1-1 Warning: bam file 15804_1_80 has no reads in window 1-1 Warning: bam file 15861_1_33 has no reads in window 1-1 Warning: bam file 15861_1_37 has no reads in window 1-1 Warning: bam file 15861_1_39 has no reads in window 1-1 Warning: bam file 15861_1_9 has no reads in window 1-1 Warning: bam file 15877_1_72 has no reads in window 1-1 Warning: bam file 15878_1_46 has no reads in window 1-1 Warning: bam file 15952_1_77 has no reads in window 1-1 Warning: bam file 15964_1_13 has no reads in window 1-1 Warning: bam file 15964_1_17 has no reads in window 1-1 Warning: bam file 15978_1_24 has no reads in window 1-1 Warning: bam file 16002_1_33 has no reads in window 1-1 Warning: bam file 16040_1_19 has no reads in window 1-1 WARNING: no bam file had any reads (after a minimum post-merging read count of 2 was imposed) in the window 601-700. Skipping to the next window.
Is this an error with the window coordinates ?
Thank you, olli
ptyr1_bam.txt ptyr1_ref.txt