Bed file error

[LliliansCalvo]

Hi I am trying to run TOGA, so far u successfully ran the first part to make the alignement. However whenever I try to run TOGA I get an error related to the bed file that I don't really know how to troubleshoot. Thanks!

./toga.py make_lastz_chains/Dmel_Cfel_2bit/Dm6.Cfel.final.chain.gz /work/FAC/FBM/Drosophila_genome/dm6.ncbiRefSeq_gxf2bed.bed /work/FAC/FBM/Drosophila_genome/dm6.2bit mod_GCA_030586385.1_ASM3058638v1_genomic.2bit --kt --pn Dmel_Cfel_results --cb 3,5 --cjn 500 --ms

ERROR:
#### Initiating TOGA class ####
# python interpreter path: /users/lcalvogo/.conda/envs/llilians_env/bin/python3
# python interpreter version: 3.10.11 (main, Apr 20 2023, 19:02:41) [GCC 11.2.0]
Version 1.1.8.dev
Commit: 97eb5a17ce76fccd9858b2ed738c51cd661292aa
Branch: master

# Python package versions
* twobitreader: unknown version
* networkx: 3.2.1
* pandas: 2.1.2
* numpy: 1.26.1
* xgboost: 2.0.1
! scikit-learn: Not installed - will try to install
* joblib: 1.3.2
* h5py: 3.10.0
Calling cmd:
/work/FAC/FBM/TOGA/./configure.sh

Compiling C code...
Model found
CESAR installation found
Command finished with exit code 0.
Does it work?
Calling cmd:
gzip -dc make_lastz_chains/Dmel_Cfel_2bit/Dm6.Cfel.final.chain.gz | /work/FAC/FBM/TOGA/./modules/chain_score_filter stdin 15000 > /work/FAC/FBM/TOGA/Dmel_Cfel_results/temp/genome_alignment.chain

Command finished with exit code 0.
filter_bed: transcript CR11023 skipped: out-of-frame transcript
filter_bed: Error! Bed file is corrupted, thickEnd MUST be >= thickStart.
Problem occurred at line 2, gene NM_078715.4
filter_bed: Error! Bed file is corrupted, thickEnd MUST be >= thickStart.
Problem occurred at line 2, gene NM_078715.4



where 
head  /work/FAC/FBM/Drosophila_genome/dm6.ncbiRefSeq_gxf2bed.bed 
chr2L	7528	9484	CR11023	0	+	7528	9484	0	2	588,1292,	0,664,
chr2L	9838	18570	NM_078715.4	0	-	17133	11214	0	9	310,160,779,1192,106,643,443,109,1506,	8422,7214,5094,3844,3681,2447,1940,1571,0,
chr2L	9838	21376	NM_001258875.2	0	-	17133	11214	0	1	311,	11227,
chr2L	9838	21376	NM_164350.3	0	-	15645	11214	0	9	311,141,779,1192,106,643,443,109,1506,	11227,10041,5094,3844,3681,2447,1940,1571,0,
chr2L	9838	21376	NM_001258873.2	0	-	17133	11214	0	9	241,160,779,1192,106,643,443,109,1506,	11297,7214,5094,3844,3681,2447,1940,1571,0,
chr2L	9838	18570	NM_164349.3	0	-	17133	11214	0	10	310,143,160,779,1192,106,643,443,109,1506,	8422,8187,7214,5094,3844,3681,2447,1940,1571,0,
chr2L	9838	21376	NM_164352.3	0	-	15645	11214	0	10	28,135,141,779,1192,106,643,443,109,1506,	11510,11227,10041,5094,3844,3681,2447,1940,1571,0,
chr2L	9838	21376	NM_001258872.2	0	-	17133	11214	0	10	241,136,160,779,1192,106,643,443,109,1506,	11297,10041,7214,5094,3844,3681,2447,1940,1571,0,
chr2L	9838	21376	NM_164348.3	0	-	19941	11214	0	9	241,136,779,1192,106,643,443,109,1506,	11297,10046,5094,3844,3681,2447,1940,1571,0,
chr2L	9838	21376	NM_164351.3	0	-	15645	11214	0	9	311,136,779,1192,106,643,443,109,1506,	11227,10041,5094,3844,3681,2447,1940,1571,0,