[2024-01-25 19:37:35,464] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:35,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:35,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8b88ec8-d69a-487b-bac5-9da22961a45d/dqc_reference
[2024-01-25 19:37:36,705] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:36,705] [INFO] Task started: Prodigal
[2024-01-25 19:37:36,706] [INFO] Running command: gunzip -c /var/lib/cwl/stg11329717-f9f0-48cb-86be-43a8185c4805/GCF_009711095.1_ASM971109v1_genomic.fna.gz | prodigal -d GCF_009711095.1_ASM971109v1_genomic.fna/cds.fna -a GCF_009711095.1_ASM971109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:46,998] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:46,999] [INFO] Task started: HMMsearch
[2024-01-25 19:37:46,999] [INFO] Running command: hmmsearch --tblout GCF_009711095.1_ASM971109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8b88ec8-d69a-487b-bac5-9da22961a45d/dqc_reference/reference_markers.hmm GCF_009711095.1_ASM971109v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:47,232] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:47,233] [INFO] Found 6/6 markers.
[2024-01-25 19:37:47,271] [INFO] Query marker FASTA was written to GCF_009711095.1_ASM971109v1_genomic.fna/markers.fasta
[2024-01-25 19:37:47,271] [INFO] Task started: Blastn
[2024-01-25 19:37:47,271] [INFO] Running command: blastn -query GCF_009711095.1_ASM971109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8b88ec8-d69a-487b-bac5-9da22961a45d/dqc_reference/reference_markers.fasta -out GCF_009711095.1_ASM971109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:48,163] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:48,166] [INFO] Selected 19 target genomes.
[2024-01-25 19:37:48,167] [INFO] Target genome list was writen to GCF_009711095.1_ASM971109v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:48,174] [INFO] Task started: fastANI
[2024-01-25 19:37:48,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg11329717-f9f0-48cb-86be-43a8185c4805/GCF_009711095.1_ASM971109v1_genomic.fna.gz --refList GCF_009711095.1_ASM971109v1_genomic.fna/target_genomes.txt --output GCF_009711095.1_ASM971109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:06,088] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:06,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8b88ec8-d69a-487b-bac5-9da22961a45d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:06,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8b88ec8-d69a-487b-bac5-9da22961a45d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:06,102] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:38:06,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:38:06,102] [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
Citrobacter rodentium	strain=NBRC 105723	GCA_000759815.1	67825	67825	type	True	82.9018	960	1539	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.8703	992	1539	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	82.831	967	1539	95	below_threshold
Citrobacter rodentium	strain=ATCC 51116	GCA_015965415.1	67825	67825	type	True	82.801	967	1539	95	below_threshold
Citrobacter amalonaticus	strain=FDAARGOS_1489	GCA_020099335.1	35703	35703	type	True	81.4886	878	1539	95	below_threshold
Citrobacter farmeri	strain=FDAARGOS 1423	GCA_019048065.1	67824	67824	type	True	81.4877	869	1539	95	below_threshold
Salmonella enterica subsp. houtenae	strain=CCUG 30041T	GCA_008692755.1	59205	28901	type	True	81.3831	751	1539	95	below_threshold
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	81.2542	795	1539	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	81.148	842	1539	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.0766	743	1539	95	below_threshold
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	81.0359	804	1539	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.0147	775	1539	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	80.9552	755	1539	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	80.8757	762	1539	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.6816	723	1539	95	below_threshold
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	80.6468	738	1539	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	80.641	751	1539	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	80.6392	736	1539	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	80.4752	685	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:06,103] [INFO] DFAST Taxonomy check result was written to GCF_009711095.1_ASM971109v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:06,104] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:06,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:06,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8b88ec8-d69a-487b-bac5-9da22961a45d/dqc_reference/checkm_data
[2024-01-25 19:38:06,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:06,152] [INFO] Task started: CheckM
[2024-01-25 19:38:06,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711095.1_ASM971109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711095.1_ASM971109v1_genomic.fna/checkm_input GCF_009711095.1_ASM971109v1_genomic.fna/checkm_result
[2024-01-25 19:38:39,097] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:39,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:39,114] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:39,114] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:39,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711095.1_ASM971109v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:39,115] [INFO] Task started: Blastn
[2024-01-25 19:38:39,115] [INFO] Running command: blastn -query GCF_009711095.1_ASM971109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8b88ec8-d69a-487b-bac5-9da22961a45d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711095.1_ASM971109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:40,603] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:40,606] [INFO] Selected 20 target genomes.
[2024-01-25 19:38:40,606] [INFO] Target genome list was writen to GCF_009711095.1_ASM971109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:40,622] [INFO] Task started: fastANI
[2024-01-25 19:38:40,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg11329717-f9f0-48cb-86be-43a8185c4805/GCF_009711095.1_ASM971109v1_genomic.fna.gz --refList GCF_009711095.1_ASM971109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711095.1_ASM971109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:02,433] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:02,448] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:02,448] [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_009711095.1	s__Escherichia_C alba	100.0	1536	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000759815.1	s__Citrobacter_A rodentium	82.8934	961	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.98	99.96	0.98	0.96	4	-
GCF_000759835.1	s__Citrobacter_A sedlakii	81.9349	901	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.16	99.00	0.95	0.93	10	-
GCF_000981805.1	s__Citrobacter_A amalonaticus_C	81.7516	900	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363175.1	s__Citrobacter_A telavivensis	81.6368	882	1539	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_900021175.1	s__Enterobacter_A timonensis	81.6059	793	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900478215.1	s__Salmonella houtenae	81.5211	753	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.09	96.71	0.94	0.89	62	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	81.4885	813	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	98.80	98.80	0.94	0.94	2	-
GCF_019048065.1	s__Citrobacter_A farmeri	81.4877	869	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.22	96.70	0.93	0.90	16	-
GCF_000006945.2	s__Salmonella enterica	81.3946	799	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	-
GCF_018323885.1	s__Citrobacter_A amalonaticus	81.3398	904	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.67	95.02	0.91	0.83	59	-
GCF_003057745.1	s__Enterobacter sp003057745	81.1922	789	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480085.1	s__Pseudescherichia sp002480085	81.1489	758	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000321045.1	s__Phytobacter massiliensis	81.1188	753	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013375935.1	s__Enterobacter cloacae_O	81.0536	794	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_000828055.2	s__Klebsiella variicola	81.0224	806	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_001888805.2	s__Enterobacter_D sp001888805	80.8912	769	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	97.70	97.19	0.94	0.94	3	-
GCF_902498915.1	s__Escherichia ruysiae	80.7631	734	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_001660175.1	s__Escherichia sp001660175	80.6406	727	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.53	99.22	0.94	0.92	3	-
GCF_003697165.2	s__Escherichia coli	80.6248	753	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:02,450] [INFO] GTDB search result was written to GCF_009711095.1_ASM971109v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:02,451] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:02,455] [INFO] DFAST_QC result json was written to GCF_009711095.1_ASM971109v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:02,455] [INFO] DFAST_QC completed!
[2024-01-25 19:39:02,455] [INFO] Total running time: 0h1m27s