Hi Quentin,
I've launched TT-Mars on HG002 assemblies (with the HG002 files downloaded from the README), and it hasn't yet finished after 1 week. Is this expected? How long should the program typically take? The input VCF has ~14K SVs (only DEL/INV/DUPs). It also hasn't written anything to file since August 8. The last file that got created is "ttmars_chrx_res.txt". The output from the tool is this (hasn't changed for 1 week):
0
1000
3000
….
9000
10000
12000
14000
0
1000
3000
…
9000
10000
12000
14000
This is the command I used (called from the TT-Mars repo):
python ttmars.py ttmars_files/HG002/ centromere_hg37.txt GRCh37-lite.fa ttmars_files/HG002_asm/h1.fa ttmars_files/HG002_asm/h2.fa hg37_tandem_repeats.bed 1 --not_hg38
Thanks!
V
Hi Quentin,
I've launched TT-Mars on HG002 assemblies (with the HG002 files downloaded from the README), and it hasn't yet finished after 1 week. Is this expected? How long should the program typically take? The input VCF has ~14K SVs (only DEL/INV/DUPs). It also hasn't written anything to file since August 8. The last file that got created is "ttmars_chrx_res.txt". The output from the tool is this (hasn't changed for 1 week):
0
1000
3000
….
9000
10000
12000
14000
0
1000
3000
…
9000
10000
12000
14000
This is the command I used (called from the TT-Mars repo):
python ttmars.py ttmars_files/HG002/ centromere_hg37.txt GRCh37-lite.fa ttmars_files/HG002_asm/h1.fa ttmars_files/HG002_asm/h2.fa hg37_tandem_repeats.bed 1 --not_hg38
Thanks!
V