[2024-01-24 12:28:35,013] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:35,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:35,018] [INFO] DQC Reference Directory: /var/lib/cwl/stgd94f054f-9ffc-45e2-a99e-d0e27f8fee5b/dqc_reference
[2024-01-24 12:28:36,224] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:36,225] [INFO] Task started: Prodigal
[2024-01-24 12:28:36,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d95e357-ec4d-46f9-bcad-c768e63e6d0a/GCF_900638065.1_55685_A01_genomic.fna.gz | prodigal -d GCF_900638065.1_55685_A01_genomic.fna/cds.fna -a GCF_900638065.1_55685_A01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:49,365] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:49,366] [INFO] Task started: HMMsearch
[2024-01-24 12:28:49,366] [INFO] Running command: hmmsearch --tblout GCF_900638065.1_55685_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd94f054f-9ffc-45e2-a99e-d0e27f8fee5b/dqc_reference/reference_markers.hmm GCF_900638065.1_55685_A01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:49,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:49,659] [INFO] Found 6/6 markers.
[2024-01-24 12:28:49,703] [INFO] Query marker FASTA was written to GCF_900638065.1_55685_A01_genomic.fna/markers.fasta
[2024-01-24 12:28:49,703] [INFO] Task started: Blastn
[2024-01-24 12:28:49,704] [INFO] Running command: blastn -query GCF_900638065.1_55685_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd94f054f-9ffc-45e2-a99e-d0e27f8fee5b/dqc_reference/reference_markers.fasta -out GCF_900638065.1_55685_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:50,529] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:50,534] [INFO] Selected 15 target genomes.
[2024-01-24 12:28:50,534] [INFO] Target genome list was writen to GCF_900638065.1_55685_A01_genomic.fna/target_genomes.txt
[2024-01-24 12:28:50,579] [INFO] Task started: fastANI
[2024-01-24 12:28:50,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d95e357-ec4d-46f9-bcad-c768e63e6d0a/GCF_900638065.1_55685_A01_genomic.fna.gz --refList GCF_900638065.1_55685_A01_genomic.fna/target_genomes.txt --output GCF_900638065.1_55685_A01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:07,701] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:07,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd94f054f-9ffc-45e2-a99e-d0e27f8fee5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:07,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd94f054f-9ffc-45e2-a99e-d0e27f8fee5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:07,717] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:29:07,717] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:29:07,717] [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 youngae	strain=NCTC13709	GCA_900638065.1	133448	133448	type	True	100.0	1622	1622	95	inconclusive
Citrobacter youngae	strain=CCUG 30791	GCA_003818115.1	133448	133448	type	True	99.9758	1573	1622	95	inconclusive
Citrobacter pasteurii	strain=FDAARGOS 1424	GCA_019047765.1	1563222	1563222	type	True	95.4172	1440	1622	95	inconclusive
Citrobacter pasteurii	strain=CIP 55.13	GCA_000826205.1	1563222	1563222	type	True	95.3887	1415	1622	95	inconclusive
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	91.8047	1369	1622	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	91.7731	1348	1622	95	below_threshold
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	91.754	1345	1622	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	90.553	1311	1622	95	below_threshold
Citrobacter europaeus	strain=97/79	GCA_900079995.3	1914243	1914243	type	True	90.4428	1344	1622	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	90.3403	1345	1622	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.9373	992	1622	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.8287	1029	1622	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	82.389	943	1622	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.9466	833	1622	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.7913	871	1622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:07,719] [INFO] DFAST Taxonomy check result was written to GCF_900638065.1_55685_A01_genomic.fna/tc_result.tsv
[2024-01-24 12:29:07,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:07,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:07,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd94f054f-9ffc-45e2-a99e-d0e27f8fee5b/dqc_reference/checkm_data
[2024-01-24 12:29:07,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:07,769] [INFO] Task started: CheckM
[2024-01-24 12:29:07,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900638065.1_55685_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900638065.1_55685_A01_genomic.fna/checkm_input GCF_900638065.1_55685_A01_genomic.fna/checkm_result
[2024-01-24 12:29:49,313] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:49,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:49,337] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:49,337] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:49,338] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900638065.1_55685_A01_genomic.fna/markers.fasta)
[2024-01-24 12:29:49,338] [INFO] Task started: Blastn
[2024-01-24 12:29:49,338] [INFO] Running command: blastn -query GCF_900638065.1_55685_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd94f054f-9ffc-45e2-a99e-d0e27f8fee5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900638065.1_55685_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:50,499] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:50,503] [INFO] Selected 15 target genomes.
[2024-01-24 12:29:50,503] [INFO] Target genome list was writen to GCF_900638065.1_55685_A01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:50,532] [INFO] Task started: fastANI
[2024-01-24 12:29:50,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d95e357-ec4d-46f9-bcad-c768e63e6d0a/GCF_900638065.1_55685_A01_genomic.fna.gz --refList GCF_900638065.1_55685_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900638065.1_55685_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:08,858] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:08,874] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:08,874] [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_003818115.1	s__Citrobacter youngae	99.9758	1573	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	conclusive
GCF_005281345.1	s__Citrobacter sp005281345	93.9768	1406	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.53	97.53	0.86	0.86	2	-
GCF_011064845.1	s__Citrobacter freundii	91.7884	1371	1622	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	91.0145	1291	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCF_002042885.1	s__Citrobacter portucalensis	90.5609	1310	1622	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	90.4428	1344	1622	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	90.3253	1346	1622	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	90.1415	1303	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	-
GCF_000155975.1	s__Citrobacter portucalensis_A	89.3803	1282	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000759755.1	s__Citrobacter werkmanii	89.2567	1302	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	96.76	96.01	0.88	0.81	67	-
GCF_001037495.1	s__Citrobacter murliniae	87.3798	1298	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.45	99.21	0.93	0.93	5	-
GCF_010231475.1	s__Citrobacter sp010231475	83.5954	1017	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981805.1	s__Citrobacter_A amalonaticus_C	83.4967	1104	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011395035.1	s__Pantoea cypripedii_A	78.7402	414	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:08,876] [INFO] GTDB search result was written to GCF_900638065.1_55685_A01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:08,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:08,880] [INFO] DFAST_QC result json was written to GCF_900638065.1_55685_A01_genomic.fna/dqc_result.json
[2024-01-24 12:30:08,880] [INFO] DFAST_QC completed!
[2024-01-24 12:30:08,880] [INFO] Total running time: 0h1m34s