No "proc_pseudogenes.bed" in the output

[xin0107]

There is no "proc_pseudogenes.bed" in the TOGA output files. At first, I found a “#” in front of the 752 line of code in toga.py, I thought I found the reason. However, after deleting "#" and re-submitting the task, there is still no "proc_pseudogenes.bed" output. I checked the function and there seems to be no problem. I don't know what's going on right now.

In addition, the content in the log file is as following, it seems that the function is not working. I don't know where the problem is, because there is no error message.

Here is the shell script I used to run TOGA: python3 /opt/service/TOGA/toga.py Zk2mm39.chain mm39.nopseudo.bed mm39.genome.2bit zk.genome.v2.1.2bit --kt --pd $work_dir/project_dir2 --pn Zk --nd $work_dir/nextflow_temp2 --nc $work_dir/nextflow_config_files --cb 30,200,350 --cjn 70 -i mm39.isoform.txt --u12 mm10.U12sites.tsv --ms

And the output files:

[xin0107]

Another ERROR： When I run “./supply/plot_mutations.py”，I got an error:

[zx_test@gatk1 Visualization]$ python3 /opt/service/TOGA/supply/plot_mutations.py mm39.nopseudo.bed inact_mut_data.hdf5 ENSMUSG00000031142 Cacna1f.v1.svg -i isoform
Traceback (most recent call last):
  File "/opt/service/TOGA/supply/plot_mutations.py", line 1270, in <module>
    args.alt_template,
  File "/opt/service/TOGA/supply/plot_mutations.py", line 1218, in make_plot
    t_picture_width = comp_width(trans_data)
  File "/opt/service/TOGA/supply/plot_mutations.py", line 754, in comp_width
    + max(UTR_WIDTH, 2 * SS_LABEL_FONTSIZE)
IndexError: list index out of range

Can you solve this problem? Thanks a lot.

[yuzhenpeng]

I have the same problems.

[xin0107]

I think TOGA may don't support that function.

[kirilenkobm]

Hi!

Adding this feature is planned in future releases.

• Bogdan

[kirilenkobm]

The recent TOGA version produces processed pseudogenes track