[2024-01-24 11:34:40,119] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,121] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e52f8ca-cead-4271-a2aa-2d80d1188ef2/dqc_reference
[2024-01-24 11:34:41,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,437] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg05832ddb-4e48-40b9-b531-bb886364cc23/GCF_013376815.1_ASM1337681v1_genomic.fna.gz | prodigal -d GCF_013376815.1_ASM1337681v1_genomic.fna/cds.fna -a GCF_013376815.1_ASM1337681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:57,668] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:57,669] [INFO] Task started: HMMsearch
[2024-01-24 11:34:57,669] [INFO] Running command: hmmsearch --tblout GCF_013376815.1_ASM1337681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e52f8ca-cead-4271-a2aa-2d80d1188ef2/dqc_reference/reference_markers.hmm GCF_013376815.1_ASM1337681v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:58,040] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:58,041] [INFO] Found 6/6 markers.
[2024-01-24 11:34:58,094] [INFO] Query marker FASTA was written to GCF_013376815.1_ASM1337681v1_genomic.fna/markers.fasta
[2024-01-24 11:34:58,095] [INFO] Task started: Blastn
[2024-01-24 11:34:58,095] [INFO] Running command: blastn -query GCF_013376815.1_ASM1337681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e52f8ca-cead-4271-a2aa-2d80d1188ef2/dqc_reference/reference_markers.fasta -out GCF_013376815.1_ASM1337681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:59,018] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:59,020] [INFO] Selected 22 target genomes.
[2024-01-24 11:34:59,021] [INFO] Target genome list was writen to GCF_013376815.1_ASM1337681v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:59,029] [INFO] Task started: fastANI
[2024-01-24 11:34:59,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg05832ddb-4e48-40b9-b531-bb886364cc23/GCF_013376815.1_ASM1337681v1_genomic.fna.gz --refList GCF_013376815.1_ASM1337681v1_genomic.fna/target_genomes.txt --output GCF_013376815.1_ASM1337681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:24,602] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:24,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e52f8ca-cead-4271-a2aa-2d80d1188ef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:24,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e52f8ca-cead-4271-a2aa-2d80d1188ef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:24,618] [INFO] Found 18 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 11:35:24,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:24,618] [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
Enterobacter cloacae	strain=DSM 30054	GCA_013376815.1	550	550	type	True	100.0	1865	1866	95	conclusive
Enterobacter cloacae	strain=FDAARGOS 1431	GCA_019047105.1	550	550	type	True	99.9978	1861	1866	95	conclusive
Enterobacter cloacae subsp. cloacae	strain=ATCC 13047	GCA_000025565.1	336306	550	type	True	99.9918	1860	1866	95	conclusive
Enterobacter cloacae	strain=ATCC 13047	GCA_000755525.1	550	550	type	True	99.9745	1836	1866	95	conclusive
Enterobacter cloacae	strain=ATCC 13047	GCA_001997105.1	550	550	type	True	99.9493	1743	1866	95	conclusive
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	99.642	1618	1866	95	conclusive
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	89.3157	1375	1866	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	89.2121	1293	1866	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	87.8537	1288	1866	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	87.7364	1336	1866	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	84.1017	1093	1866	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	84.0954	1085	1866	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.3944	51	1866	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	78.9972	545	1866	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	78.916	535	1866	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	78.916	459	1866	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	78.7521	514	1866	95	below_threshold
Edwardsiella piscicida	strain=ACC35.1	GCA_001896205.1	1263550	1263550	reftype	True	78.0807	348	1866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:24,620] [INFO] DFAST Taxonomy check result was written to GCF_013376815.1_ASM1337681v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:24,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:24,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:24,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e52f8ca-cead-4271-a2aa-2d80d1188ef2/dqc_reference/checkm_data
[2024-01-24 11:35:24,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:24,678] [INFO] Task started: CheckM
[2024-01-24 11:35:24,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013376815.1_ASM1337681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013376815.1_ASM1337681v1_genomic.fna/checkm_input GCF_013376815.1_ASM1337681v1_genomic.fna/checkm_result
[2024-01-24 11:36:15,376] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:15,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:15,395] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:15,395] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:15,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013376815.1_ASM1337681v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:15,396] [INFO] Task started: Blastn
[2024-01-24 11:36:15,396] [INFO] Running command: blastn -query GCF_013376815.1_ASM1337681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e52f8ca-cead-4271-a2aa-2d80d1188ef2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013376815.1_ASM1337681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:16,624] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:16,628] [INFO] Selected 33 target genomes.
[2024-01-24 11:36:16,628] [INFO] Target genome list was writen to GCF_013376815.1_ASM1337681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:16,652] [INFO] Task started: fastANI
[2024-01-24 11:36:16,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg05832ddb-4e48-40b9-b531-bb886364cc23/GCF_013376815.1_ASM1337681v1_genomic.fna.gz --refList GCF_013376815.1_ASM1337681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013376815.1_ASM1337681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:50,482] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:50,504] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:50,504] [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_000025565.1	s__Enterobacter cloacae	99.9918	1861	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	conclusive
GCF_002939185.1	s__Enterobacter sichuanensis	89.2199	1319	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_007035645.1	s__Enterobacter asburiae_B	89.113	1361	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_001729805.1	s__Enterobacter roggenkampii	89.086	1319	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_001521715.1	s__Enterobacter asburiae	89.0828	1306	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_003634515.1	s__Enterobacter asburiae_A	89.0	1329	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_009755685.1	s__Enterobacter sp000568095	88.9777	1330	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_900324475.1	s__Enterobacter bugandensis	88.8257	1330	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_008364625.1	s__Enterobacter dykesii	88.8247	1287	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_008080435.1	s__Enterobacter asburiae_C	88.821	1325	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_011754535.1	s__Enterobacter cloacae_N	88.7222	1368	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_008364555.1	s__Enterobacter vonholyi	88.6954	1277	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_001729765.1	s__Enterobacter kobei	88.6125	1357	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_003046225.1	s__Enterobacter cloacae_I	88.4496	1305	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.61	95.47	0.89	0.86	14	-
GCF_001750725.1	s__Enterobacter ludwigii	88.3418	1350	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.79	98.47	0.93	0.83	88	-
GCF_014169315.1	s__Enterobacter cloacae_P	87.8174	1219	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.13	99.10	0.85	0.85	3	-
GCF_900322725.1	s__Enterobacter quasihormaechei	87.6411	1316	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_019047785.1	s__Enterobacter cancerogenus	86.8111	1234	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.78	98.42	0.93	0.90	16	-
GCF_011290365.1	s__Leclercia sp003024485	84.5535	1142	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.06	98.06	0.90	0.90	2	-
GCF_017348915.1	s__UBA7405 sp000755535	84.1247	1088	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	98.56	97.85	0.93	0.89	10	-
GCF_009363175.1	s__Citrobacter_A telavivensis	82.2798	963	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010231475.1	s__Citrobacter sp010231475	81.2158	854	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261615.1	s__Kosakonia sp018261615	81.1938	878	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095535.1	s__Pantoea cypripedii	79.3641	541	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_014946725.1	s__Pantoea mediterraneensis_A	79.2162	380	1866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:50,506] [INFO] GTDB search result was written to GCF_013376815.1_ASM1337681v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:50,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:50,510] [INFO] DFAST_QC result json was written to GCF_013376815.1_ASM1337681v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:50,510] [INFO] DFAST_QC completed!
[2024-01-24 11:36:50,511] [INFO] Total running time: 0h2m10s