fixed error for teflon_collapse.py but getting an error in teflon_genotype.py about teflon HOT 2 CLOSED

Hi, I am no longer getting this error but the genotype folder is empty despite the program saying it's finished.

Below is my joblog:

(teflon_env) [hyangg@n1826 TEFLON]$ python ./teflon_genotype.py \

-wd $HOME/project-vlsork/TEFLON/
-d $HOME/project-vlsork/TEFLON/qlob.prep_TF/
-s $HOME/project-vlsork/TEFLON/samples.txt
-dt "pooled"
Lower-bound coverage threshold filters corresponding to samples ['ANG.5', 'WOO.4.w6'] is [1, 1]
NOTE: all sites with adjusted read counts > upper-bound coverage threshold will be marked -9
Upper-bound coverage threshold filters corresponding to samples ['ANG.5', 'WOO.4.w6'] is [82, 366]
NOTE: all sites with adjusted read counts > upper-bound coverage threshold will be marked -9
cdm: gunzip -c /u/home/h/hyangg/project-vlsork/TEFLON/qlob.prep_TF/qlob.pseudo2ref.pickle.gz > /u/home/h/hyangg/project-vlsork/TEFLON/qlob.prep_TF/qlob.pseudo2ref.pickle.gz.tmp
loading pickle: /u/home/h/hyangg/project-vlsork/TEFLON/qlob.prep_TF/qlob.pseudo2ref.pickle.gz.tmp
NOTE: this step can be time and memory intensive for large reference genomes
pickle loaded!
Converting coordinates from pseudospace to reference-based coordinates...
Traceback (most recent call last):
File "./teflon_genotype.py", line 122, in
main()
File "./teflon_genotype.py", line 116, in main
pt.pt_portal(countDir,genoDir,samples, posMap, stats, p2rC, l_thresh, h_thresh)
File "/u/project/vlsork/hyangg/TEFLON/teflon_scripts/genotyper_poolType.py", line 51, in pt_portal
p2rC.pseudo2refConvert_portal(outFILE1,posMap,outFILE2)
File "/u/project/vlsork/hyangg/TEFLON/teflon_scripts/pseudo2refConvert.py", line 50, in pseudo2refConvert_portal
ls[2]=pseudoMap[chrom][int(ls[2])]
IndexError: list index out of range

from teflon.

I solved the issue - RepeatMasker annotates for satellite repeats and low-complexity repeats in addition to TEs, but these were not in my TE hierarchy text. You can probably find a way to include them in the workflow but once I removed those from my TE reference bed file and re-ran the reference prep step everything worked smoothly.

from teflon.