[2024-01-24 13:57:43,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fb1fb00-ec14-44b0-a6b3-8b08cfa6523d/dqc_reference
[2024-01-24 13:57:45,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,385] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,385] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6331bb2-3950-4c05-95d3-c199fe9f9e18/GCF_004353845.1_ASM435384v1_genomic.fna.gz | prodigal -d GCF_004353845.1_ASM435384v1_genomic.fna/cds.fna -a GCF_004353845.1_ASM435384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:00,397] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:00,397] [INFO] Task started: HMMsearch
[2024-01-24 13:58:00,397] [INFO] Running command: hmmsearch --tblout GCF_004353845.1_ASM435384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fb1fb00-ec14-44b0-a6b3-8b08cfa6523d/dqc_reference/reference_markers.hmm GCF_004353845.1_ASM435384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:00,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:00,729] [INFO] Found 6/6 markers.
[2024-01-24 13:58:00,773] [INFO] Query marker FASTA was written to GCF_004353845.1_ASM435384v1_genomic.fna/markers.fasta
[2024-01-24 13:58:00,773] [INFO] Task started: Blastn
[2024-01-24 13:58:00,774] [INFO] Running command: blastn -query GCF_004353845.1_ASM435384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fb1fb00-ec14-44b0-a6b3-8b08cfa6523d/dqc_reference/reference_markers.fasta -out GCF_004353845.1_ASM435384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:01,644] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:01,647] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:01,648] [INFO] Target genome list was writen to GCF_004353845.1_ASM435384v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:01,659] [INFO] Task started: fastANI
[2024-01-24 13:58:01,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6331bb2-3950-4c05-95d3-c199fe9f9e18/GCF_004353845.1_ASM435384v1_genomic.fna.gz --refList GCF_004353845.1_ASM435384v1_genomic.fna/target_genomes.txt --output GCF_004353845.1_ASM435384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:22,462] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:22,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fb1fb00-ec14-44b0-a6b3-8b08cfa6523d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:22,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fb1fb00-ec14-44b0-a6b3-8b08cfa6523d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:22,479] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:22,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:22,479] [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 arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	100.0	1786	1789	95	conclusive
Citrobacter europaeus	strain=97/79	GCA_900079995.3	1914243	1914243	type	True	94.2255	1464	1789	95	below_threshold
Citrobacter braakii	strain=FDAARGOS 1421	GCA_019048805.1	57706	57706	type	True	93.011	1419	1789	95	below_threshold
Citrobacter braakii	strain=ATCC 51113	GCA_002075345.1	57706	57706	type	True	92.9518	1412	1789	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	92.8456	1412	1789	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	92.5797	1436	1789	95	below_threshold
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	92.4961	1427	1789	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	92.4923	1424	1789	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_000734905.1	546	546	type	True	92.4333	1378	1789	95	below_threshold
Citrobacter pasteurii	strain=FDAARGOS 1424	GCA_019047765.1	1563222	1563222	type	True	89.8757	1336	1789	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	83.0673	1047	1789	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	83.0659	1009	1789	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	82.0618	864	1789	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.8968	860	1789	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.7705	891	1789	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	81.5979	787	1789	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	81.4525	808	1789	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:22,483] [INFO] DFAST Taxonomy check result was written to GCF_004353845.1_ASM435384v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:22,485] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:22,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:22,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fb1fb00-ec14-44b0-a6b3-8b08cfa6523d/dqc_reference/checkm_data
[2024-01-24 13:58:22,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:22,561] [INFO] Task started: CheckM
[2024-01-24 13:58:22,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004353845.1_ASM435384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004353845.1_ASM435384v1_genomic.fna/checkm_input GCF_004353845.1_ASM435384v1_genomic.fna/checkm_result
[2024-01-24 13:59:11,422] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:11,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:11,444] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:11,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:11,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004353845.1_ASM435384v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:11,446] [INFO] Task started: Blastn
[2024-01-24 13:59:11,446] [INFO] Running command: blastn -query GCF_004353845.1_ASM435384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fb1fb00-ec14-44b0-a6b3-8b08cfa6523d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004353845.1_ASM435384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:12,564] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:12,567] [INFO] Selected 12 target genomes.
[2024-01-24 13:59:12,567] [INFO] Target genome list was writen to GCF_004353845.1_ASM435384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:12,576] [INFO] Task started: fastANI
[2024-01-24 13:59:12,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6331bb2-3950-4c05-95d3-c199fe9f9e18/GCF_004353845.1_ASM435384v1_genomic.fna.gz --refList GCF_004353845.1_ASM435384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004353845.1_ASM435384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:26,954] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:26,967] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:26,967] [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_004353845.1	s__Citrobacter freundii_E	100.0	1785	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	conclusive
GCF_900079995.3	s__Citrobacter europaeus	94.2255	1464	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
GCF_002075345.1	s__Citrobacter braakii	92.9518	1412	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	-
GCF_002042885.1	s__Citrobacter portucalensis	92.8456	1412	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_011064845.1	s__Citrobacter freundii	92.5797	1436	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	-
GCF_018035235.1	s__Citrobacter freundii_A	91.6204	1403	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCF_000155975.1	s__Citrobacter portucalensis_A	91.2556	1404	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003818115.1	s__Citrobacter youngae	90.0523	1343	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	-
GCA_900759445.1	s__Klebsiella sp900759445	87.1692	752	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363175.1	s__Citrobacter_A telavivensis	83.6528	1148	1789	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	83.4218	1069	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017348915.1	s__UBA7405 sp000755535	81.4525	808	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	98.56	97.85	0.93	0.89	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,969] [INFO] GTDB search result was written to GCF_004353845.1_ASM435384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:26,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:26,974] [INFO] DFAST_QC result json was written to GCF_004353845.1_ASM435384v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:26,974] [INFO] DFAST_QC completed!
[2024-01-24 13:59:26,974] [INFO] Total running time: 0h1m43s