[2024-01-24 13:27:58,252] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,254] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,254] [INFO] DQC Reference Directory: /var/lib/cwl/stg03756c1d-6b96-4f9c-986c-7103c34b0e2c/dqc_reference
[2024-01-24 13:27:59,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,436] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,437] [INFO] Running command: gunzip -c /var/lib/cwl/stg770f7993-926e-454c-99f6-1455ae000ab0/GCF_020341495.1_ASM2034149v1_genomic.fna.gz | prodigal -d GCF_020341495.1_ASM2034149v1_genomic.fna/cds.fna -a GCF_020341495.1_ASM2034149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:13,491] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:13,491] [INFO] Task started: HMMsearch
[2024-01-24 13:28:13,491] [INFO] Running command: hmmsearch --tblout GCF_020341495.1_ASM2034149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03756c1d-6b96-4f9c-986c-7103c34b0e2c/dqc_reference/reference_markers.hmm GCF_020341495.1_ASM2034149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:13,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:13,762] [INFO] Found 6/6 markers.
[2024-01-24 13:28:13,807] [INFO] Query marker FASTA was written to GCF_020341495.1_ASM2034149v1_genomic.fna/markers.fasta
[2024-01-24 13:28:13,808] [INFO] Task started: Blastn
[2024-01-24 13:28:13,808] [INFO] Running command: blastn -query GCF_020341495.1_ASM2034149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03756c1d-6b96-4f9c-986c-7103c34b0e2c/dqc_reference/reference_markers.fasta -out GCF_020341495.1_ASM2034149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:14,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:14,747] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:14,747] [INFO] Target genome list was writen to GCF_020341495.1_ASM2034149v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:14,756] [INFO] Task started: fastANI
[2024-01-24 13:28:14,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg770f7993-926e-454c-99f6-1455ae000ab0/GCF_020341495.1_ASM2034149v1_genomic.fna.gz --refList GCF_020341495.1_ASM2034149v1_genomic.fna/target_genomes.txt --output GCF_020341495.1_ASM2034149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:35,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:35,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03756c1d-6b96-4f9c-986c-7103c34b0e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:35,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03756c1d-6b96-4f9c-986c-7103c34b0e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:35,362] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:35,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:35,362] [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	91.3241	1415	1668	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	91.2712	1442	1668	95	below_threshold
Citrobacter braakii	strain=FDAARGOS 1421	GCA_019048805.1	57706	57706	type	True	91.0915	1381	1668	95	below_threshold
Citrobacter braakii	strain=ATCC 51113	GCA_002075345.1	57706	57706	type	True	91.0499	1362	1668	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	91.0466	1350	1668	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	90.9711	1397	1668	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	90.8827	1381	1668	95	below_threshold
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	90.8534	1385	1668	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_000734905.1	546	546	type	True	90.8427	1325	1668	95	below_threshold
Citrobacter youngae	strain=NCTC13709	GCA_900638065.1	133448	133448	type	True	89.3484	1312	1668	95	below_threshold
Citrobacter youngae	strain=CCUG 30791	GCA_003818115.1	133448	133448	type	True	89.2524	1291	1668	95	below_threshold
Citrobacter pasteurii	strain=FDAARGOS 1424	GCA_019047765.1	1563222	1563222	type	True	89.185	1307	1668	95	below_threshold
Citrobacter pasteurii	strain=CIP 55.13	GCA_000826205.1	1563222	1563222	type	True	89.1045	1282	1668	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	83.3675	1008	1668	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	83.207	1031	1668	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.704	879	1668	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.5118	869	1668	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.4717	862	1668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:35,364] [INFO] DFAST Taxonomy check result was written to GCF_020341495.1_ASM2034149v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:35,364] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:35,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:35,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03756c1d-6b96-4f9c-986c-7103c34b0e2c/dqc_reference/checkm_data
[2024-01-24 13:28:35,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:35,414] [INFO] Task started: CheckM
[2024-01-24 13:28:35,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020341495.1_ASM2034149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020341495.1_ASM2034149v1_genomic.fna/checkm_input GCF_020341495.1_ASM2034149v1_genomic.fna/checkm_result
[2024-01-24 13:29:16,735] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:16,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:16,753] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:16,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:16,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020341495.1_ASM2034149v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:16,754] [INFO] Task started: Blastn
[2024-01-24 13:29:16,754] [INFO] Running command: blastn -query GCF_020341495.1_ASM2034149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03756c1d-6b96-4f9c-986c-7103c34b0e2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_020341495.1_ASM2034149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:18,094] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:18,098] [INFO] Selected 11 target genomes.
[2024-01-24 13:29:18,098] [INFO] Target genome list was writen to GCF_020341495.1_ASM2034149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:18,108] [INFO] Task started: fastANI
[2024-01-24 13:29:18,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg770f7993-926e-454c-99f6-1455ae000ab0/GCF_020341495.1_ASM2034149v1_genomic.fna.gz --refList GCF_020341495.1_ASM2034149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020341495.1_ASM2034149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:30,876] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:30,886] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:30,886] [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	99.981	1634	1668	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	93.0742	1393	1668	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	91.3171	1415	1668	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	91.2736	1440	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_002075345.1	s__Citrobacter braakii	91.0499	1362	1668	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	91.0466	1350	1668	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	90.9728	1397	1668	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	90.1632	1346	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCF_003818115.1	s__Citrobacter youngae	89.2524	1291	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	-
GCF_005281345.1	s__Citrobacter sp005281345	88.5921	1294	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.53	97.53	0.86	0.86	2	-
GCA_900759445.1	s__Klebsiella sp900759445	85.8564	728	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:30,888] [INFO] GTDB search result was written to GCF_020341495.1_ASM2034149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:30,888] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:30,892] [INFO] DFAST_QC result json was written to GCF_020341495.1_ASM2034149v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:30,892] [INFO] DFAST_QC completed!
[2024-01-24 13:29:30,892] [INFO] Total running time: 0h1m33s