[2024-01-24 14:15:02,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,578] [INFO] DQC Reference Directory: /var/lib/cwl/stga484c4dc-af13-4a80-8a63-cfb7bcc9a4b5/dqc_reference
[2024-01-24 14:15:03,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:03,868] [INFO] Task started: Prodigal
[2024-01-24 14:15:03,868] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1de7d2e-f8f8-43f3-8381-15a7fc7cc987/GCF_003818115.1_ASM381811v1_genomic.fna.gz | prodigal -d GCF_003818115.1_ASM381811v1_genomic.fna/cds.fna -a GCF_003818115.1_ASM381811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:17,418] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:17,419] [INFO] Task started: HMMsearch
[2024-01-24 14:15:17,419] [INFO] Running command: hmmsearch --tblout GCF_003818115.1_ASM381811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga484c4dc-af13-4a80-8a63-cfb7bcc9a4b5/dqc_reference/reference_markers.hmm GCF_003818115.1_ASM381811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:17,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:17,738] [INFO] Found 6/6 markers.
[2024-01-24 14:15:17,786] [INFO] Query marker FASTA was written to GCF_003818115.1_ASM381811v1_genomic.fna/markers.fasta
[2024-01-24 14:15:17,787] [INFO] Task started: Blastn
[2024-01-24 14:15:17,787] [INFO] Running command: blastn -query GCF_003818115.1_ASM381811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga484c4dc-af13-4a80-8a63-cfb7bcc9a4b5/dqc_reference/reference_markers.fasta -out GCF_003818115.1_ASM381811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:18,696] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:18,700] [INFO] Selected 15 target genomes.
[2024-01-24 14:15:18,700] [INFO] Target genome list was writen to GCF_003818115.1_ASM381811v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:18,716] [INFO] Task started: fastANI
[2024-01-24 14:15:18,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1de7d2e-f8f8-43f3-8381-15a7fc7cc987/GCF_003818115.1_ASM381811v1_genomic.fna.gz --refList GCF_003818115.1_ASM381811v1_genomic.fna/target_genomes.txt --output GCF_003818115.1_ASM381811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:36,267] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:36,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga484c4dc-af13-4a80-8a63-cfb7bcc9a4b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:36,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga484c4dc-af13-4a80-8a63-cfb7bcc9a4b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:36,279] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:15:36,279] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:15:36,280] [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=CCUG 30791	GCA_003818115.1	133448	133448	type	True	100.0	1576	1578	95	inconclusive
Citrobacter youngae	strain=NCTC13709	GCA_900638065.1	133448	133448	type	True	99.9899	1577	1578	95	inconclusive
Citrobacter pasteurii	strain=CIP 55.13	GCA_000826205.1	1563222	1563222	type	True	95.4225	1387	1578	95	inconclusive
Citrobacter pasteurii	strain=FDAARGOS 1424	GCA_019047765.1	1563222	1563222	type	True	95.4133	1399	1578	95	inconclusive
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	91.7413	1333	1578	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	91.697	1347	1578	95	below_threshold
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	91.6964	1337	1578	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	90.5594	1292	1578	95	below_threshold
Citrobacter europaeus	strain=97/79	GCA_900079995.3	1914243	1914243	type	True	90.3895	1334	1578	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	90.1698	1324	1578	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.7186	1011	1578	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.6867	950	1578	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	82.2848	921	1578	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.7313	824	1578	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.5226	847	1578	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:36,281] [INFO] DFAST Taxonomy check result was written to GCF_003818115.1_ASM381811v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:36,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:36,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:36,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga484c4dc-af13-4a80-8a63-cfb7bcc9a4b5/dqc_reference/checkm_data
[2024-01-24 14:15:36,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:36,328] [INFO] Task started: CheckM
[2024-01-24 14:15:36,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003818115.1_ASM381811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003818115.1_ASM381811v1_genomic.fna/checkm_input GCF_003818115.1_ASM381811v1_genomic.fna/checkm_result
[2024-01-24 14:16:18,701] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:18,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:18,722] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:18,723] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:18,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003818115.1_ASM381811v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:18,724] [INFO] Task started: Blastn
[2024-01-24 14:16:18,724] [INFO] Running command: blastn -query GCF_003818115.1_ASM381811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga484c4dc-af13-4a80-8a63-cfb7bcc9a4b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003818115.1_ASM381811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:19,970] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:19,974] [INFO] Selected 15 target genomes.
[2024-01-24 14:16:19,974] [INFO] Target genome list was writen to GCF_003818115.1_ASM381811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:19,984] [INFO] Task started: fastANI
[2024-01-24 14:16:19,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1de7d2e-f8f8-43f3-8381-15a7fc7cc987/GCF_003818115.1_ASM381811v1_genomic.fna.gz --refList GCF_003818115.1_ASM381811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003818115.1_ASM381811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:38,085] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:38,101] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:38,101] [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	100.0	1576	1578	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	93.9943	1390	1578	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	91.702	1346	1578	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	91.0312	1285	1578	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	90.5675	1291	1578	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	90.3895	1334	1578	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	90.2103	1285	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	-
GCF_004353845.1	s__Citrobacter freundii_E	90.1611	1325	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_000155975.1	s__Citrobacter portucalensis_A	89.2888	1279	1578	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	89.2152	1296	1578	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	87.1892	1276	1578	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	83.5424	1006	1578	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	83.3084	1080	1578	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	78.6512	416	1578	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 14:16:38,103] [INFO] GTDB search result was written to GCF_003818115.1_ASM381811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:38,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:38,107] [INFO] DFAST_QC result json was written to GCF_003818115.1_ASM381811v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:38,107] [INFO] DFAST_QC completed!
[2024-01-24 14:16:38,107] [INFO] Total running time: 0h1m36s