Could not split CESAR jobs

[AgustoLuz]

High I am running, when I run in my data I got the error "Could not split CESAR jobs".
I run the following line:

./toga.py make_lastz_chains/make_lastz_chains/chicken_turkey/target.query.final.chain.gz ../chicken/genes.bed12 ../chicken/galGal6.2bit ../turkey/melGal5.2bit --pn chicken_turkey_test --kt --cjn 100 --cb 3,5 --ces --cjn 500 --m --cesar_mem_limit 300

I have attached the log file.
toga_2023_11_13_at_20_05.log

[kirilenkobm]

Hi @AgustoLuz

I apologize for the long delay in responding. Thank you for reporting the issue, t's the first problem reported with this module. Could you please execute the following command:

/nas2/aluzuriaganeira/birds/TOGA/./split_exon_realign_jobs.py /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/trans_to_chain_classes.tsv /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/toga_filt_ref_annot.bed /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/toga_filt_ref_annot.hdf5 /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/genome_alignment.bst /nas2/aluzuriaganeira/birds/chicken/galGal6.2bit /nas2/aluzuriaganeira/birds/turkey/melGal5.2bit /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test --jobs_dir /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/cesar_jobs --jobs_num 500 --combined /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/cesar_combined --results /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/cesar_results --buckets 8,16,32,64,128,256,512,999 --mem_limit 300 --chains_limit 100 --skipped_genes /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/rejected/SPLIT_CESAR.txt --rejected_log /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/rejected --cesar_binary /nas2/aluzuriaganeira/birds/TOGA/./CESAR2.0/cesar --paralogs_log /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/paralogs.txt --uhq_flank 50 --predefined_glp_class_path /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/predefined_glp_cesar_split.tsv --unprocessed_log /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/technical_cesar_err --log_file /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/toga_2023_11_13_at_20_05.log --cesar_logs_dir /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp_logs --mask_stops --check_loss /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/inact_mut_data --fragments_data /nas2/aluzuriaganeira/birds/TOGA/chicken_turkey_test/temp/gene_fragments.txt

and share the console output with me, assuming you haven't deleted the output directory? Regrettably, the logging for this module isn't working as expected, but I plan to fix it in the upcoming update."