Nura7177
commented
3 months ago I split 1900 into two subsets and ran --identify on 900+ genomes. It worked will and did not generate this error. However, now I have two directories and two sets of marker genes gtdbtk.bac120.markers_summary.tsv in each of them. How and at which stage is it possible to combine them to build them all in one tree?
Hi, @pchaumeil, Pierre,
while running --identify on 1800 bacteria complete genomes (test script on one genome worked well and did not generate this error), got the error below, markers_summary.tsv were not generated and, thus, we cannot proceed further with --align:
Traceback (most recent call last): File "/trinity/home/anaconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/external/prodigal.py", line 221, in run raise ProdigalException('Prodigal returned a non-zero exit code.') gtdbtk.exceptions.ProdigalException: Prodigal returned a non-zero exit code.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/trinity/home/anaconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/main.py", line 102, in main gt_parser.parse_options(args) File "/trinity/home/anaconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/main.py", line 1188, in parse_options self.identify(options) File "/trinity/home/anaconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/main.py", line 319, in identify reports = markers.identify(genomes, File "/trinity/home/anaconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/markers.py", line 205, in identify genome_dictionary = prodigal.run(genomes, tln_tables) File "/trinity/home/anaconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/external/prodigal.py", line 230, in run raise ProdigalException(f'An exception was caught while running Prodigal: {e}') gtdbtk.exceptions.ProdigalException: An exception was caught while running Prodigal: Prodigal returned a non-zero exit code.
gtdbtk.ar53.markers_summary.tsv gtdbtk.bac120.markers_summary.tsv gtdbtk.failed_genomes.tsv gtdbtk.translation_table_summary.tsv
were not generated
Environment
conda list && conda list --revisions) Conda_list.txtDebugging information
gtdbtk.loghas been included (drag and drop the file to upload)GTDBtk_2.4.0_log.txt
GCA_900637955.1_54424_G02_genomic.fna GCA_000503915.1_ASM50391v1_genomic.fna
GCA_002865995.1_ASM286599v1_genomic.fna
GCA_900637975.1_53550_F01_genomic.fna
Additional comments
all the genomes were processed and directories created: genomes_gtdbtk/ident_out_2/identify/intermediate_results/marker_genes
genomes_gtdbtk/ident_out_2/identify/intermediate_results/marker_genes/GCA_900637975.1_53550_F01_genomic]$ls GCA_900637975.1_53550_F01_genomic_protein.faa GCA_900637975.1_53550_F01_genomic_protein.fna GCA_900637975.1_53550_F01_genomic_protein.gff prodigal_translation_table.tsv GCA_900637975.1_53550_F01_genomic_protein.faa.sha256 GCA_900637975.1_53550_F01_genomic_protein.fna.sha256 GCA_900637975.1_53550_F01_genomic_protein.gff.sha256 prodigal_translation_table.tsv.sha256