Error in Step 8, merge_cesar_jobs: CRITICAL: could not extract any bed lines from the CESAR output, abort

[shuifeng1988]

I perform a wide-scale test using the recommonded scripts " ./toga.py test_input/hg38.mm10.chr11.chain test_input/hg38.genCode27.chr11.bed test_input/hg38.2bit test_input/mm10.2bit --kt --pn test -i supply/hg38.wgEncodeGencodeCompV34.isoforms.txt --nc ./nextflow_config_files --cb 3,5 --cjn 500 --u12 supply/hg38.U12sites.tsv --ms", But error occurs in step7 and step8, no outputs in step7, even the step6 is OK!
Error in step8,

STEP 6: Create processed pseudogenes track

Creating processed pseudogenes track.
make_pr_pseudogenes_anno: loading chain index...
make_pr_pseudogenes anno: 8 transcripts have processed pseudogenes
make_pr_pseudogenes anno: identifying processed pseudogenes regions in the query
make_pr_pseudogenes anno: analysing data for 8 reference transcripts
make_pr_pseudogenes anno: for 8 reference transcripts found 8 processed pseudogene chains in total
make_pr_pseudogenes anno: resulted in 8 processed pseudogenes projections in query
make_pr_pseudogenes_anno: generating bed lines for 8 projections
make_pr_pseudogenes_anno: generated 8 intervals
make_pr_pseudogenes anno: collapsing intersecting bed lines (if any)
make_pr_pseudogenes anno: 8 records before collapse
make_pr_pseudogenes anno: 2 records after collapse
make_pr_pseudogenes_anno: generated 2 bed lines to be saved
make_pr_pseudogenes_anno: 2 processed pseudogene annotations in total
make_pr_pseudogenes_anno: saving results to /home/shuifeng/git/TOGA/test/proc_pseudogenes.bed

STEP 7: Execute CESAR jobs: parallel step

Pushing 2 CESAR job lists
Pushing memory bucket 3Gb to the executor
Selected parallelization strategy: nextflow
Parallel manager: pushing job nextflow /home/shuifeng/git/TOGA/execute_joblist.nf --joblist /home/shuifeng/git/TOGA/test/temp/cesar_joblist_queue_3.txt -c /home/shuifeng/git/TOGA/test/temp/cesar_config_3_queue.nf
Pushing memory bucket 5Gb to the executor
Selected parallelization strategy: nextflow
Parallel manager: pushing job nextflow /home/shuifeng/git/TOGA/execute_joblist.nf --joblist /home/shuifeng/git/TOGA/test/temp/cesar_joblist_queue_5.txt -c /home/shuifeng/git/TOGA/test/temp/cesar_config_5_queue.nf

Stated polling cluster jobs until they done

CESAR jobs done

Checking whether all CESAR results are complete
No CESAR jobs crashed according to rejection log
Logs from individual CESAR jobs are show below

STEP 8: Merge STEP 7 output

Merging CESAR output to make fasta and bed files.
merge_cesar_jobs: module called with arguments:

• input_dir: /home/shuifeng/git/TOGA/test/temp/cesar_results
• output_bed: /home/shuifeng/git/TOGA/test/temp/intermediate.bed
• output_fasta: /home/shuifeng/git/TOGA/test/nucleotide.fasta
• meta_data_arg: /home/shuifeng/git/TOGA/test/temp/exons_meta_data.tsv
• skipped_arg: /home/shuifeng/git/TOGA/test/temp/rejected/CESAR_MERGE.txt
• prot_arg: /home/shuifeng/git/TOGA/test/prot.fasta
• codon_arg: /home/shuifeng/git/TOGA/test/codon.fasta
• output_trash: /home/shuifeng/git/TOGA/test/temp/trash_exons.bed
• fragm_data: /home/shuifeng/git/TOGA/test/temp/bed_fragments_to_exons.tsv
• exclude: None
  merge_cesar_jobs: merging CESAR results from 0 output files
  merge_cesar_jobs: Saving the output
  merge_cesar_jobs: CRITICAL: could not extract any bed lines from the CESAR output, abort

[ReverendCasy]

Hello,
Could you please attach the TOGA running log? Also, could you also check the CESAR output directories in temp?