[2024-01-24 14:46:52,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:52,324] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:52,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e017e74-f530-49aa-bfda-4a2fe4ef4ecf/dqc_reference
[2024-01-24 14:46:55,363] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:55,365] [INFO] Task started: Prodigal
[2024-01-24 14:46:55,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg52681ff0-deaa-4ca5-ab9d-35cde732d685/GCF_002923025.1_ASM292302v1_genomic.fna.gz | prodigal -d GCF_002923025.1_ASM292302v1_genomic.fna/cds.fna -a GCF_002923025.1_ASM292302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:09,159] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:09,159] [INFO] Task started: HMMsearch
[2024-01-24 14:47:09,159] [INFO] Running command: hmmsearch --tblout GCF_002923025.1_ASM292302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e017e74-f530-49aa-bfda-4a2fe4ef4ecf/dqc_reference/reference_markers.hmm GCF_002923025.1_ASM292302v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:09,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:09,503] [INFO] Found 6/6 markers.
[2024-01-24 14:47:09,545] [INFO] Query marker FASTA was written to GCF_002923025.1_ASM292302v1_genomic.fna/markers.fasta
[2024-01-24 14:47:09,545] [INFO] Task started: Blastn
[2024-01-24 14:47:09,545] [INFO] Running command: blastn -query GCF_002923025.1_ASM292302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e017e74-f530-49aa-bfda-4a2fe4ef4ecf/dqc_reference/reference_markers.fasta -out GCF_002923025.1_ASM292302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:10,573] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:10,579] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:10,579] [INFO] Target genome list was writen to GCF_002923025.1_ASM292302v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:10,587] [INFO] Task started: fastANI
[2024-01-24 14:47:10,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg52681ff0-deaa-4ca5-ab9d-35cde732d685/GCF_002923025.1_ASM292302v1_genomic.fna.gz --refList GCF_002923025.1_ASM292302v1_genomic.fna/target_genomes.txt --output GCF_002923025.1_ASM292302v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:28,119] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:28,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e017e74-f530-49aa-bfda-4a2fe4ef4ecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:28,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e017e74-f530-49aa-bfda-4a2fe4ef4ecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:28,133] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:28,133] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:28,133] [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
Lelliottia aquatilis	strain=6331-17	GCA_002923025.1	2080838	2080838	type	True	100.0	1567	1571	95	conclusive
Lelliottia nimipressuralis	strain=CCUG 25894	GCA_004115925.1	69220	69220	type	True	89.9229	1284	1571	95	below_threshold
Lelliottia amnigena	strain=LMG 2784	GCA_002553545.1	61646	61646	type	True	85.8137	1137	1571	95	below_threshold
Lelliottia amnigena	strain=FDAARGOS 1444	GCA_019047465.1	61646	61646	type	True	85.8048	1172	1571	95	below_threshold
Lelliottia amnigena	strain=NBRC 105700	GCA_001514515.1	61646	61646	type	True	85.7629	1170	1571	95	below_threshold
Enterobacter quasimori	strain=090044	GCA_003964905.1	2838947	2838947	type	True	84.859	1125	1571	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	84.7945	1149	1571	95	below_threshold
Enterobacter oligotrophicus	strain=CCA6	GCA_009176645.1	2478464	2478464	type	True	84.7708	1147	1571	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	84.6898	1067	1571	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	84.6709	1116	1571	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	84.5515	1099	1571	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	84.503	1099	1571	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	84.4944	1073	1571	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	84.4689	1127	1571	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	83.396	1023	1571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:28,135] [INFO] DFAST Taxonomy check result was written to GCF_002923025.1_ASM292302v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:28,136] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:28,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:28,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e017e74-f530-49aa-bfda-4a2fe4ef4ecf/dqc_reference/checkm_data
[2024-01-24 14:47:28,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:28,183] [INFO] Task started: CheckM
[2024-01-24 14:47:28,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002923025.1_ASM292302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002923025.1_ASM292302v1_genomic.fna/checkm_input GCF_002923025.1_ASM292302v1_genomic.fna/checkm_result
[2024-01-24 14:48:11,232] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:11,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:11,253] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:11,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:11,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002923025.1_ASM292302v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:11,254] [INFO] Task started: Blastn
[2024-01-24 14:48:11,255] [INFO] Running command: blastn -query GCF_002923025.1_ASM292302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e017e74-f530-49aa-bfda-4a2fe4ef4ecf/dqc_reference/reference_markers_gtdb.fasta -out GCF_002923025.1_ASM292302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:12,819] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:12,823] [INFO] Selected 15 target genomes.
[2024-01-24 14:48:12,823] [INFO] Target genome list was writen to GCF_002923025.1_ASM292302v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:12,875] [INFO] Task started: fastANI
[2024-01-24 14:48:12,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg52681ff0-deaa-4ca5-ab9d-35cde732d685/GCF_002923025.1_ASM292302v1_genomic.fna.gz --refList GCF_002923025.1_ASM292302v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002923025.1_ASM292302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:29,763] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:29,778] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:29,779] [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
GCA_002271215.1	s__Lelliottia jeotgali	98.815	1410	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.81	98.80	0.92	0.92	9	conclusive
GCF_004115925.1	s__Lelliottia nimipressuralis	89.9229	1284	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.29	98.00	0.93	0.92	11	-
GCA_009668015.1	s__Lelliottia sp009668015	86.9124	1161	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016325.1	s__Lelliottia sp000016325	85.8809	1190	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	95.60	95.60	0.93	0.93	2	-
GCA_900635465.1	s__Lelliottia amnigena	85.7883	1168	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.81	98.20	0.95	0.91	15	-
GCF_009755685.1	s__Enterobacter sp000568095	84.8214	1124	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_003594935.1	s__Enterobacter huaxiensis	84.8189	1157	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.98	98.98	0.94	0.94	2	-
GCF_004331265.1	s__Enterobacter wuhouensis	84.8034	1148	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364625.1	s__Enterobacter dykesii	84.778	1111	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_009176645.1	s__Enterobacter oligotrophicus	84.7776	1146	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.55	99.09	0.97	0.94	3	-
GCF_003634515.1	s__Enterobacter asburiae_A	84.7634	1129	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_003594915.1	s__Enterobacter chuandaensis	84.5776	1113	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	98.32	0.92	0.92	3	-
GCF_000211415.1	s__Enterobacter mori	84.5582	1098	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.59	96.13	0.88	0.85	23	-
GCF_004402045.1	s__Enterobacter nimipressuralis_A	84.5004	1111	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057745.1	s__Enterobacter sp003057745	84.2748	1074	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:29,780] [INFO] GTDB search result was written to GCF_002923025.1_ASM292302v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:29,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:29,785] [INFO] DFAST_QC result json was written to GCF_002923025.1_ASM292302v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:29,785] [INFO] DFAST_QC completed!
[2024-01-24 14:48:29,786] [INFO] Total running time: 0h1m37s