[2023-06-19 09:28:52,987] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:28:52,990] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:28:52,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg2172547f-0e28-49c3-8a35-5ab925419629/dqc_reference
[2023-06-19 09:28:54,213] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:28:54,213] [INFO] Task started: Prodigal
[2023-06-19 09:28:54,214] [INFO] Running command: gunzip -c /var/lib/cwl/stg29848029-807b-4ee3-ba85-bc90a53a7e0b/GCA_018376975.1_ASM1837697v1_genomic.fna.gz | prodigal -d GCA_018376975.1_ASM1837697v1_genomic.fna/cds.fna -a GCA_018376975.1_ASM1837697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:29:05,160] [INFO] Task succeeded: Prodigal
[2023-06-19 09:29:05,161] [INFO] Task started: HMMsearch
[2023-06-19 09:29:05,161] [INFO] Running command: hmmsearch --tblout GCA_018376975.1_ASM1837697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2172547f-0e28-49c3-8a35-5ab925419629/dqc_reference/reference_markers.hmm GCA_018376975.1_ASM1837697v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:29:05,444] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:29:05,453] [INFO] Found 6/6 markers.
[2023-06-19 09:29:05,529] [INFO] Query marker FASTA was written to GCA_018376975.1_ASM1837697v1_genomic.fna/markers.fasta
[2023-06-19 09:29:05,530] [INFO] Task started: Blastn
[2023-06-19 09:29:05,530] [INFO] Running command: blastn -query GCA_018376975.1_ASM1837697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2172547f-0e28-49c3-8a35-5ab925419629/dqc_reference/reference_markers.fasta -out GCA_018376975.1_ASM1837697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:29:06,346] [INFO] Task succeeded: Blastn
[2023-06-19 09:29:06,352] [INFO] Selected 11 target genomes.
[2023-06-19 09:29:06,352] [INFO] Target genome list was writen to GCA_018376975.1_ASM1837697v1_genomic.fna/target_genomes.txt
[2023-06-19 09:29:06,357] [INFO] Task started: fastANI
[2023-06-19 09:29:06,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg29848029-807b-4ee3-ba85-bc90a53a7e0b/GCA_018376975.1_ASM1837697v1_genomic.fna.gz --refList GCA_018376975.1_ASM1837697v1_genomic.fna/target_genomes.txt --output GCA_018376975.1_ASM1837697v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:29:19,362] [INFO] Task succeeded: fastANI
[2023-06-19 09:29:19,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2172547f-0e28-49c3-8a35-5ab925419629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:29:19,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2172547f-0e28-49c3-8a35-5ab925419629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:29:19,383] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-19 09:29:19,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 09:29:19,384] [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 freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	97.456	1190	1372	95	conclusive
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	97.4272	1196	1372	95	conclusive
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	97.4097	1204	1372	95	conclusive
Citrobacter freundii	strain=ATCC 8090	GCA_000734905.1	546	546	type	True	97.4043	1159	1372	95	conclusive
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	94.6854	1172	1372	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	92.4922	1178	1372	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.5363	872	1372	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.5303	829	1372	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.8307	744	1372	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.6193	733	1372	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.5352	753	1372	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:29:19,387] [INFO] DFAST Taxonomy check result was written to GCA_018376975.1_ASM1837697v1_genomic.fna/tc_result.tsv
[2023-06-19 09:29:19,388] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:29:19,388] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:29:19,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2172547f-0e28-49c3-8a35-5ab925419629/dqc_reference/checkm_data
[2023-06-19 09:29:19,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:29:19,436] [INFO] Task started: CheckM
[2023-06-19 09:29:19,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376975.1_ASM1837697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376975.1_ASM1837697v1_genomic.fna/checkm_input GCA_018376975.1_ASM1837697v1_genomic.fna/checkm_result
[2023-06-19 09:29:56,596] [INFO] Task succeeded: CheckM
[2023-06-19 09:29:56,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.34%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 09:29:56,628] [INFO] ===== Completeness check finished =====
[2023-06-19 09:29:56,628] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:29:56,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376975.1_ASM1837697v1_genomic.fna/markers.fasta)
[2023-06-19 09:29:56,629] [INFO] Task started: Blastn
[2023-06-19 09:29:56,629] [INFO] Running command: blastn -query GCA_018376975.1_ASM1837697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2172547f-0e28-49c3-8a35-5ab925419629/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376975.1_ASM1837697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:29:57,950] [INFO] Task succeeded: Blastn
[2023-06-19 09:29:57,957] [INFO] Selected 10 target genomes.
[2023-06-19 09:29:57,957] [INFO] Target genome list was writen to GCA_018376975.1_ASM1837697v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:29:57,996] [INFO] Task started: fastANI
[2023-06-19 09:29:57,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg29848029-807b-4ee3-ba85-bc90a53a7e0b/GCA_018376975.1_ASM1837697v1_genomic.fna.gz --refList GCA_018376975.1_ASM1837697v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376975.1_ASM1837697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:30:09,106] [INFO] Task succeeded: fastANI
[2023-06-19 09:30:09,125] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:30:09,125] [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_011064845.1	s__Citrobacter freundii	97.3954	1205	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	conclusive
GCF_002042885.1	s__Citrobacter portucalensis	94.6854	1172	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_900079995.3	s__Citrobacter europaeus	92.747	1166	1372	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	92.4922	1178	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_018035235.1	s__Citrobacter freundii_A	92.4219	1161	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCF_002075345.1	s__Citrobacter braakii	92.3636	1148	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	-
GCF_003818115.1	s__Citrobacter youngae	91.6174	1138	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	-
GCA_000759755.1	s__Citrobacter werkmanii	90.6894	1145	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	96.76	96.01	0.88	0.81	67	-
GCF_000155975.1	s__Citrobacter portucalensis_A	90.5594	1121	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900759445.1	s__Klebsiella sp900759445	86.0574	622	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 09:30:09,128] [INFO] GTDB search result was written to GCA_018376975.1_ASM1837697v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:30:09,128] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:30:09,134] [INFO] DFAST_QC result json was written to GCA_018376975.1_ASM1837697v1_genomic.fna/dqc_result.json
[2023-06-19 09:30:09,135] [INFO] DFAST_QC completed!
[2023-06-19 09:30:09,135] [INFO] Total running time: 0h1m16s