[2024-01-24 11:42:20,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg018a68e0-1bd2-411a-8e7f-216d13bf18d3/dqc_reference
[2024-01-24 11:42:24,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg47ccef4f-6be9-45c3-83ac-e0ccabc2a6e8/GCF_008802955.1_ASM880295v1_genomic.fna.gz | prodigal -d GCF_008802955.1_ASM880295v1_genomic.fna/cds.fna -a GCF_008802955.1_ASM880295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:38,670] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:38,670] [INFO] Task started: HMMsearch
[2024-01-24 11:42:38,670] [INFO] Running command: hmmsearch --tblout GCF_008802955.1_ASM880295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg018a68e0-1bd2-411a-8e7f-216d13bf18d3/dqc_reference/reference_markers.hmm GCF_008802955.1_ASM880295v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:38,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:38,989] [INFO] Found 6/6 markers.
[2024-01-24 11:42:39,038] [INFO] Query marker FASTA was written to GCF_008802955.1_ASM880295v1_genomic.fna/markers.fasta
[2024-01-24 11:42:39,039] [INFO] Task started: Blastn
[2024-01-24 11:42:39,039] [INFO] Running command: blastn -query GCF_008802955.1_ASM880295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg018a68e0-1bd2-411a-8e7f-216d13bf18d3/dqc_reference/reference_markers.fasta -out GCF_008802955.1_ASM880295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:39,875] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:39,879] [INFO] Selected 17 target genomes.
[2024-01-24 11:42:39,879] [INFO] Target genome list was writen to GCF_008802955.1_ASM880295v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:39,886] [INFO] Task started: fastANI
[2024-01-24 11:42:39,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ccef4f-6be9-45c3-83ac-e0ccabc2a6e8/GCF_008802955.1_ASM880295v1_genomic.fna.gz --refList GCF_008802955.1_ASM880295v1_genomic.fna/target_genomes.txt --output GCF_008802955.1_ASM880295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:42:58,639] [INFO] Task succeeded: fastANI
[2024-01-24 11:42:58,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg018a68e0-1bd2-411a-8e7f-216d13bf18d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:42:58,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg018a68e0-1bd2-411a-8e7f-216d13bf18d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:42:58,654] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:42:58,654] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:42:58,654] [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 europaeus	strain=97/79	GCA_900079995.3	1914243	1914243	type	True	91.1138	1402	1706	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	91.0957	1418	1706	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	90.9447	1348	1706	95	below_threshold
Citrobacter braakii	strain=ATCC 51113	GCA_002075345.1	57706	57706	type	True	90.9216	1361	1706	95	below_threshold
Citrobacter braakii	strain=FDAARGOS 1421	GCA_019048805.1	57706	57706	type	True	90.9008	1371	1706	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	90.7562	1376	1706	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	90.7263	1370	1706	95	below_threshold
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	90.7253	1368	1706	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_000734905.1	546	546	type	True	90.6528	1332	1706	95	below_threshold
Citrobacter youngae	strain=CCUG 30791	GCA_003818115.1	133448	133448	type	True	89.1276	1317	1706	95	below_threshold
Citrobacter youngae	strain=NCTC13709	GCA_900638065.1	133448	133448	type	True	89.1106	1338	1706	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	83.0975	1014	1706	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.9797	1055	1706	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.7453	884	1706	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.6425	862	1706	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.6146	891	1706	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.5895	862	1706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:42:58,656] [INFO] DFAST Taxonomy check result was written to GCF_008802955.1_ASM880295v1_genomic.fna/tc_result.tsv
[2024-01-24 11:42:58,656] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:42:58,656] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:42:58,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg018a68e0-1bd2-411a-8e7f-216d13bf18d3/dqc_reference/checkm_data
[2024-01-24 11:42:58,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:42:58,706] [INFO] Task started: CheckM
[2024-01-24 11:42:58,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802955.1_ASM880295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802955.1_ASM880295v1_genomic.fna/checkm_input GCF_008802955.1_ASM880295v1_genomic.fna/checkm_result
[2024-01-24 11:43:42,723] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:42,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:42,755] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:42,755] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:42,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802955.1_ASM880295v1_genomic.fna/markers.fasta)
[2024-01-24 11:43:42,756] [INFO] Task started: Blastn
[2024-01-24 11:43:42,757] [INFO] Running command: blastn -query GCF_008802955.1_ASM880295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg018a68e0-1bd2-411a-8e7f-216d13bf18d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802955.1_ASM880295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:43,949] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:43,953] [INFO] Selected 13 target genomes.
[2024-01-24 11:43:43,953] [INFO] Target genome list was writen to GCF_008802955.1_ASM880295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:43:43,962] [INFO] Task started: fastANI
[2024-01-24 11:43:43,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ccef4f-6be9-45c3-83ac-e0ccabc2a6e8/GCF_008802955.1_ASM880295v1_genomic.fna.gz --refList GCF_008802955.1_ASM880295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802955.1_ASM880295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:43:58,697] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:58,715] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:43:58,715] [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_000759755.1	s__Citrobacter werkmanii	96.3583	1427	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	96.76	96.01	0.88	0.81	67	conclusive
GCF_000155975.1	s__Citrobacter portucalensis_A	93.2464	1373	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900079995.3	s__Citrobacter europaeus	91.1047	1403	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
GCF_004353845.1	s__Citrobacter freundii_E	91.0957	1418	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_002042885.1	s__Citrobacter portucalensis	90.9447	1348	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_002075345.1	s__Citrobacter braakii	90.9096	1362	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	-
GCF_011064845.1	s__Citrobacter freundii	90.7542	1377	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	-
GCF_003818115.1	s__Citrobacter youngae	89.1165	1319	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	-
GCF_015672735.1	s__Citrobacter sp015672735	86.978	1273	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759445.1	s__Klebsiella sp900759445	85.8548	733	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900322725.1	s__Enterobacter quasihormaechei	82.0011	854	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_013375935.1	s__Enterobacter cloacae_O	81.6113	861	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_001975225.1	s__Kosakonia cowanii	80.7131	739	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	97.51	95.65	0.94	0.87	21	-
--------------------------------------------------------------------------------
[2024-01-24 11:43:58,717] [INFO] GTDB search result was written to GCF_008802955.1_ASM880295v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:43:58,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:43:58,721] [INFO] DFAST_QC result json was written to GCF_008802955.1_ASM880295v1_genomic.fna/dqc_result.json
[2024-01-24 11:43:58,722] [INFO] DFAST_QC completed!
[2024-01-24 11:43:58,722] [INFO] Total running time: 0h1m38s