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