[2024-01-25 20:21:50,653] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:50,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:50,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg32e834fc-2fe3-4d22-a657-1718df06686e/dqc_reference
[2024-01-25 20:21:51,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:51,745] [INFO] Task started: Prodigal
[2024-01-25 20:21:51,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg50662259-37ab-48c6-ab79-a7788f2c01e8/GCF_012932875.1_ASM1293287v1_genomic.fna.gz | prodigal -d GCF_012932875.1_ASM1293287v1_genomic.fna/cds.fna -a GCF_012932875.1_ASM1293287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:01,579] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:01,579] [INFO] Task started: HMMsearch
[2024-01-25 20:22:01,579] [INFO] Running command: hmmsearch --tblout GCF_012932875.1_ASM1293287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32e834fc-2fe3-4d22-a657-1718df06686e/dqc_reference/reference_markers.hmm GCF_012932875.1_ASM1293287v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:01,791] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:01,792] [INFO] Found 6/6 markers.
[2024-01-25 20:22:01,822] [INFO] Query marker FASTA was written to GCF_012932875.1_ASM1293287v1_genomic.fna/markers.fasta
[2024-01-25 20:22:01,823] [INFO] Task started: Blastn
[2024-01-25 20:22:01,823] [INFO] Running command: blastn -query GCF_012932875.1_ASM1293287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32e834fc-2fe3-4d22-a657-1718df06686e/dqc_reference/reference_markers.fasta -out GCF_012932875.1_ASM1293287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:02,673] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:02,676] [INFO] Selected 11 target genomes.
[2024-01-25 20:22:02,677] [INFO] Target genome list was writen to GCF_012932875.1_ASM1293287v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:02,691] [INFO] Task started: fastANI
[2024-01-25 20:22:02,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg50662259-37ab-48c6-ab79-a7788f2c01e8/GCF_012932875.1_ASM1293287v1_genomic.fna.gz --refList GCF_012932875.1_ASM1293287v1_genomic.fna/target_genomes.txt --output GCF_012932875.1_ASM1293287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:14,630] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:14,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32e834fc-2fe3-4d22-a657-1718df06686e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:14,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32e834fc-2fe3-4d22-a657-1718df06686e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:14,639] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:22:14,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:14,639] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Brenneria salicis	strain=ATCC 15712	GCA_012932875.1	55214	55214	type	True	100.0	1343	1348	95	conclusive
Brenneria salicis	strain=DSM 30166	GCA_003666165.1	55214	55214	type	True	99.9353	1257	1348	95	conclusive
Brenneria salicis	strain=DSM 30166	GCA_003315515.1	55214	55214	type	True	99.9331	1255	1348	95	conclusive
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	85.6574	959	1348	95	below_threshold
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	85.4833	966	1348	95	below_threshold
Brenneria alni	strain=NCPPB 3934	GCA_003666245.1	71656	71656	type	True	81.7706	784	1348	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	80.8298	694	1348	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	80.7733	690	1348	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.6514	365	1348	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.4981	394	1348	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.168	338	1348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:14,642] [INFO] DFAST Taxonomy check result was written to GCF_012932875.1_ASM1293287v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:14,643] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:14,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:14,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32e834fc-2fe3-4d22-a657-1718df06686e/dqc_reference/checkm_data
[2024-01-25 20:22:14,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:14,694] [INFO] Task started: CheckM
[2024-01-25 20:22:14,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012932875.1_ASM1293287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012932875.1_ASM1293287v1_genomic.fna/checkm_input GCF_012932875.1_ASM1293287v1_genomic.fna/checkm_result
[2024-01-25 20:22:46,501] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:46,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:46,520] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:46,520] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:46,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012932875.1_ASM1293287v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:46,521] [INFO] Task started: Blastn
[2024-01-25 20:22:46,521] [INFO] Running command: blastn -query GCF_012932875.1_ASM1293287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32e834fc-2fe3-4d22-a657-1718df06686e/dqc_reference/reference_markers_gtdb.fasta -out GCF_012932875.1_ASM1293287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:47,816] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:47,819] [INFO] Selected 8 target genomes.
[2024-01-25 20:22:47,819] [INFO] Target genome list was writen to GCF_012932875.1_ASM1293287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:47,829] [INFO] Task started: fastANI
[2024-01-25 20:22:47,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg50662259-37ab-48c6-ab79-a7788f2c01e8/GCF_012932875.1_ASM1293287v1_genomic.fna.gz --refList GCF_012932875.1_ASM1293287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012932875.1_ASM1293287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:56,350] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:56,357] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:56,357] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003315515.1	s__Brenneria salicis	99.9331	1255	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.99	99.99	1.00	0.99	3	conclusive
GCF_003115845.1	s__Brenneria roseae	85.6452	960	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	96.57	96.57	0.91	0.91	2	-
GCF_005484945.1	s__Brenneria rubrifaciens	84.3883	947	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155275.1	s__Brenneria sp013155275	82.0771	878	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.39	99.39	0.93	0.93	2	-
GCF_003666245.1	s__Brenneria alni	81.7911	781	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005484965.1	s__Brenneria nigrifluens	81.7705	856	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	98.35	95.07	0.92	0.76	4	-
GCF_017569925.1	s__Brenneria izadpanahii	81.3302	770	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002307355.1	s__Pectobacterium polaris	80.915	678	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:56,358] [INFO] GTDB search result was written to GCF_012932875.1_ASM1293287v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:56,359] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:56,363] [INFO] DFAST_QC result json was written to GCF_012932875.1_ASM1293287v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:56,363] [INFO] DFAST_QC completed!
[2024-01-25 20:22:56,363] [INFO] Total running time: 0h1m6s