[2024-01-25 19:00:35,495] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:35,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:35,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a516a99-223f-4b46-b3e6-055bc33f254c/dqc_reference
[2024-01-25 19:00:36,623] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:36,623] [INFO] Task started: Prodigal
[2024-01-25 19:00:36,624] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dfcda91-872c-4f1b-9f11-a3fefa854176/GCF_024023655.1_ASM2402365v1_genomic.fna.gz | prodigal -d GCF_024023655.1_ASM2402365v1_genomic.fna/cds.fna -a GCF_024023655.1_ASM2402365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:49,186] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:49,186] [INFO] Task started: HMMsearch
[2024-01-25 19:00:49,186] [INFO] Running command: hmmsearch --tblout GCF_024023655.1_ASM2402365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a516a99-223f-4b46-b3e6-055bc33f254c/dqc_reference/reference_markers.hmm GCF_024023655.1_ASM2402365v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:49,486] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:49,487] [INFO] Found 6/6 markers.
[2024-01-25 19:00:49,536] [INFO] Query marker FASTA was written to GCF_024023655.1_ASM2402365v1_genomic.fna/markers.fasta
[2024-01-25 19:00:49,537] [INFO] Task started: Blastn
[2024-01-25 19:00:49,537] [INFO] Running command: blastn -query GCF_024023655.1_ASM2402365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a516a99-223f-4b46-b3e6-055bc33f254c/dqc_reference/reference_markers.fasta -out GCF_024023655.1_ASM2402365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:50,354] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:50,359] [INFO] Selected 18 target genomes.
[2024-01-25 19:00:50,359] [INFO] Target genome list was writen to GCF_024023655.1_ASM2402365v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:50,366] [INFO] Task started: fastANI
[2024-01-25 19:00:50,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dfcda91-872c-4f1b-9f11-a3fefa854176/GCF_024023655.1_ASM2402365v1_genomic.fna.gz --refList GCF_024023655.1_ASM2402365v1_genomic.fna/target_genomes.txt --output GCF_024023655.1_ASM2402365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:09,992] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:09,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a516a99-223f-4b46-b3e6-055bc33f254c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:09,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a516a99-223f-4b46-b3e6-055bc33f254c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:10,004] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:01:10,004] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:01:10,005] [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=ATCC 8090	GCA_011064845.1	546	546	type	True	92.7463	1382	1765	95	below_threshold
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	92.6965	1367	1765	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	92.6493	1392	1765	95	below_threshold
Citrobacter braakii	strain=FDAARGOS 1421	GCA_019048805.1	57706	57706	type	True	92.0515	1351	1765	95	below_threshold
Citrobacter braakii	strain=ATCC 51113	GCA_002075345.1	57706	57706	type	True	92.0306	1357	1765	95	below_threshold
Citrobacter europaeus	strain=97/79	GCA_900079995.3	1914243	1914243	type	True	91.8101	1387	1765	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	91.5162	1420	1765	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	91.2445	1357	1765	95	below_threshold
Citrobacter pasteurii	strain=FDAARGOS 1424	GCA_019047765.1	1563222	1563222	type	True	90.9764	1291	1765	95	below_threshold
Citrobacter youngae	strain=CCUG 30791	GCA_003818115.1	133448	133448	type	True	90.9585	1276	1765	95	below_threshold
Citrobacter pasteurii	strain=CIP 55.13	GCA_000826205.1	1563222	1563222	type	True	90.9481	1294	1765	95	below_threshold
Citrobacter youngae	strain=NCTC13709	GCA_900638065.1	133448	133448	type	True	90.8487	1304	1765	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.7364	981	1765	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.6598	1018	1765	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.5451	841	1765	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.5254	848	1765	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.5205	842	1765	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.4623	858	1765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:10,006] [INFO] DFAST Taxonomy check result was written to GCF_024023655.1_ASM2402365v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:10,006] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:10,007] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:10,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a516a99-223f-4b46-b3e6-055bc33f254c/dqc_reference/checkm_data
[2024-01-25 19:01:10,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:10,059] [INFO] Task started: CheckM
[2024-01-25 19:01:10,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024023655.1_ASM2402365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024023655.1_ASM2402365v1_genomic.fna/checkm_input GCF_024023655.1_ASM2402365v1_genomic.fna/checkm_result
[2024-01-25 19:01:48,628] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:48,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:48,648] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:48,648] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:48,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024023655.1_ASM2402365v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:48,649] [INFO] Task started: Blastn
[2024-01-25 19:01:48,649] [INFO] Running command: blastn -query GCF_024023655.1_ASM2402365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a516a99-223f-4b46-b3e6-055bc33f254c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024023655.1_ASM2402365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:49,800] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:49,802] [INFO] Selected 14 target genomes.
[2024-01-25 19:01:49,803] [INFO] Target genome list was writen to GCF_024023655.1_ASM2402365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:49,808] [INFO] Task started: fastANI
[2024-01-25 19:01:49,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dfcda91-872c-4f1b-9f11-a3fefa854176/GCF_024023655.1_ASM2402365v1_genomic.fna.gz --refList GCF_024023655.1_ASM2402365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024023655.1_ASM2402365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:05,237] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:05,247] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:05,247] [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_018035235.1	s__Citrobacter freundii_A	99.3549	1556	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	conclusive
GCF_011064845.1	s__Citrobacter freundii	92.7463	1382	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	-
GCF_002075345.1	s__Citrobacter braakii	92.0406	1356	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	-
GCF_900079995.3	s__Citrobacter europaeus	91.8101	1387	1765	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	91.5226	1420	1765	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	91.2321	1358	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_003818115.1	s__Citrobacter youngae	90.9585	1276	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	-
GCF_000155975.1	s__Citrobacter portucalensis_A	90.1568	1346	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015672735.1	s__Citrobacter sp015672735	86.7753	1269	1765	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	86.4955	713	1765	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	81.4951	858	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_011290365.1	s__Leclercia sp003024485	81.3262	834	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.06	98.06	0.90	0.90	2	-
GCA_902706205.1	s__Scandinavium sp902706205	80.4256	761	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111105.1	s__Rosenbergiella nectarea	78.1397	101	1765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:05,252] [INFO] GTDB search result was written to GCF_024023655.1_ASM2402365v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:05,253] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:05,261] [INFO] DFAST_QC result json was written to GCF_024023655.1_ASM2402365v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:05,261] [INFO] DFAST_QC completed!
[2024-01-25 19:02:05,261] [INFO] Total running time: 0h1m30s