[2024-01-24 13:36:45,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d856f64-4d83-4418-af1c-f0e30669b908/dqc_reference
[2024-01-24 13:36:47,046] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,047] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,047] [INFO] Running command: gunzip -c /var/lib/cwl/stg18bb0797-6de0-4a8a-9722-a1e91ab9f93f/GCF_000321045.1_ASM32104v2_genomic.fna.gz | prodigal -d GCF_000321045.1_ASM32104v2_genomic.fna/cds.fna -a GCF_000321045.1_ASM32104v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:00,758] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:00,758] [INFO] Task started: HMMsearch
[2024-01-24 13:37:00,759] [INFO] Running command: hmmsearch --tblout GCF_000321045.1_ASM32104v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d856f64-4d83-4418-af1c-f0e30669b908/dqc_reference/reference_markers.hmm GCF_000321045.1_ASM32104v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:01,049] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:01,050] [INFO] Found 6/6 markers.
[2024-01-24 13:37:01,090] [INFO] Query marker FASTA was written to GCF_000321045.1_ASM32104v2_genomic.fna/markers.fasta
[2024-01-24 13:37:01,090] [INFO] Task started: Blastn
[2024-01-24 13:37:01,091] [INFO] Running command: blastn -query GCF_000321045.1_ASM32104v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d856f64-4d83-4418-af1c-f0e30669b908/dqc_reference/reference_markers.fasta -out GCF_000321045.1_ASM32104v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:02,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:02,026] [INFO] Selected 29 target genomes.
[2024-01-24 13:37:02,027] [INFO] Target genome list was writen to GCF_000321045.1_ASM32104v2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:02,035] [INFO] Task started: fastANI
[2024-01-24 13:37:02,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg18bb0797-6de0-4a8a-9722-a1e91ab9f93f/GCF_000321045.1_ASM32104v2_genomic.fna.gz --refList GCF_000321045.1_ASM32104v2_genomic.fna/target_genomes.txt --output GCF_000321045.1_ASM32104v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:31,217] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:31,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d856f64-4d83-4418-af1c-f0e30669b908/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:31,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d856f64-4d83-4418-af1c-f0e30669b908/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:31,241] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:31,242] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:31,242] [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 wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.8677	862	1651	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.7868	869	1651	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030	GCA_000751755.1	1667327	1463165	type	True	81.7777	831	1651	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.766	860	1651	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.7394	850	1651	95	below_threshold
Citrobacter rodentium	strain=NBRC 105723	GCA_000759815.1	67825	67825	type	True	81.7368	845	1651	95	below_threshold
Citrobacter rodentium	strain=ATCC 51116	GCA_015965415.1	67825	67825	type	True	81.7226	862	1651	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	81.7066	849	1651	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	81.7004	862	1651	95	below_threshold
Klebsiella quasipneumoniae	strain=DSM 28211	GCA_020115515.1	1463165	1463165	type	True	81.6817	842	1651	95	below_threshold
Klebsiella quasipneumoniae	strain=FDAARGOS_1503	GCA_020099175.1	1463165	1463165	type	True	81.6703	844	1651	95	below_threshold
Enterobacter hormaechei subsp. xiangfangensis	strain=LMG27195	GCA_001729785.1	1296536	158836	type	True	81.5281	884	1651	95	below_threshold
Pseudescherichia vulneris	strain=NCTC12130	GCA_900450975.1	566	566	type	True	81.52	895	1651	95	below_threshold
Pseudescherichia vulneris	strain=NBRC 102420	GCA_000759795.1	566	566	type	True	81.5125	877	1651	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.4553	868	1651	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	81.4316	925	1651	95	below_threshold
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	81.3108	864	1651	95	below_threshold
Citrobacter amalonaticus	strain=JCM 1661	GCA_018323885.1	35703	35703	type	True	81.2648	791	1651	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	81.2039	832	1651	95	below_threshold
Citrobacter amalonaticus	strain=FDAARGOS_1489	GCA_020099335.1	35703	35703	type	True	81.1751	806	1651	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	81.0679	854	1651	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	81.0158	847	1651	95	below_threshold
Salmonella enterica	strain=FDAARGOS_878	GCA_016028495.1	28901	28901	type	True	80.9747	763	1651	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	80.9694	838	1651	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	80.9544	763	1651	95	below_threshold
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	80.9008	766	1651	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	80.8992	812	1651	95	below_threshold
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	80.8695	764	1651	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	80.687	705	1651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:31,244] [INFO] DFAST Taxonomy check result was written to GCF_000321045.1_ASM32104v2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:31,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:31,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:31,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d856f64-4d83-4418-af1c-f0e30669b908/dqc_reference/checkm_data
[2024-01-24 13:37:31,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:31,296] [INFO] Task started: CheckM
[2024-01-24 13:37:31,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000321045.1_ASM32104v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000321045.1_ASM32104v2_genomic.fna/checkm_input GCF_000321045.1_ASM32104v2_genomic.fna/checkm_result
[2024-01-24 13:38:12,268] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:12,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:12,287] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:12,287] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:12,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000321045.1_ASM32104v2_genomic.fna/markers.fasta)
[2024-01-24 13:38:12,287] [INFO] Task started: Blastn
[2024-01-24 13:38:12,287] [INFO] Running command: blastn -query GCF_000321045.1_ASM32104v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d856f64-4d83-4418-af1c-f0e30669b908/dqc_reference/reference_markers_gtdb.fasta -out GCF_000321045.1_ASM32104v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:13,690] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:13,694] [INFO] Selected 20 target genomes.
[2024-01-24 13:38:13,694] [INFO] Target genome list was writen to GCF_000321045.1_ASM32104v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:13,706] [INFO] Task started: fastANI
[2024-01-24 13:38:13,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg18bb0797-6de0-4a8a-9722-a1e91ab9f93f/GCF_000321045.1_ASM32104v2_genomic.fna.gz --refList GCF_000321045.1_ASM32104v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000321045.1_ASM32104v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:33,353] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:33,371] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:33,371] [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_000321045.1	s__Phytobacter massiliensis	99.9999	1643	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_004346725.1	s__Phytobacter diazotrophicus	82.7655	1072	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	98.52	97.53	0.93	0.89	19	-
GCA_901456055.1	s__Phytobacter ursingii	82.6007	1065	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	97.10	96.01	0.86	0.80	7	-
GCA_900112785.1	s__Phytobacter palmae	82.4966	1027	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900021175.1	s__Enterobacter_A timonensis	82.0749	866	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	81.8303	836	1651	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_007035645.1	s__Enterobacter asburiae_B	81.8271	863	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_900322725.1	s__Enterobacter quasihormaechei	81.7928	863	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_000759815.1	s__Citrobacter_A rodentium	81.7427	843	1651	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_008364625.1	s__Enterobacter dykesii	81.7081	850	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_003634515.1	s__Enterobacter asburiae_A	81.6857	892	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_000493015.1	s__Enterobacter sp000493015	81.6373	872	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.7595	98.68	98.68	0.92	0.92	2	-
GCF_002918705.1	s__Pseudescherichia sp002918705	81.555	914	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.58	97.76	0.93	0.92	5	-
GCF_001729745.1	s__Enterobacter hormaechei_A	81.5367	868	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	-
GCF_900116015.1	s__Enterobacter_D sp900116015	81.4664	911	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	97.94	97.83	0.93	0.90	7	-
GCF_001297775.1	s__Trabulsiella odontotermitis	81.1719	806	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	99.98	99.97	0.99	0.99	5	-
GCF_000759835.1	s__Citrobacter_A sedlakii	81.1651	827	1651	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_000006945.2	s__Salmonella enterica	80.9478	763	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	-
GCF_000696575.1	s__Siccibacter colletis	80.9237	808	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009907385.1	s__Atlantibacter hermannii_A	80.8845	768	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:33,373] [INFO] GTDB search result was written to GCF_000321045.1_ASM32104v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:33,374] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:33,379] [INFO] DFAST_QC result json was written to GCF_000321045.1_ASM32104v2_genomic.fna/dqc_result.json
[2024-01-24 13:38:33,380] [INFO] DFAST_QC completed!
[2024-01-24 13:38:33,380] [INFO] Total running time: 0h1m48s