[2024-01-25 18:46:35,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:35,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:35,647] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb7c20dd-148b-4252-b4b0-dd843bb5e9b8/dqc_reference
[2024-01-25 18:46:36,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:36,756] [INFO] Task started: Prodigal
[2024-01-25 18:46:36,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg049df084-a0ed-469f-8fb6-48321370330f/GCF_900079995.3_ASM90007999v3_genomic.fna.gz | prodigal -d GCF_900079995.3_ASM90007999v3_genomic.fna/cds.fna -a GCF_900079995.3_ASM90007999v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:49,311] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:49,312] [INFO] Task started: HMMsearch
[2024-01-25 18:46:49,312] [INFO] Running command: hmmsearch --tblout GCF_900079995.3_ASM90007999v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb7c20dd-148b-4252-b4b0-dd843bb5e9b8/dqc_reference/reference_markers.hmm GCF_900079995.3_ASM90007999v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:49,624] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:49,626] [INFO] Found 6/6 markers.
[2024-01-25 18:46:49,674] [INFO] Query marker FASTA was written to GCF_900079995.3_ASM90007999v3_genomic.fna/markers.fasta
[2024-01-25 18:46:49,674] [INFO] Task started: Blastn
[2024-01-25 18:46:49,674] [INFO] Running command: blastn -query GCF_900079995.3_ASM90007999v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb7c20dd-148b-4252-b4b0-dd843bb5e9b8/dqc_reference/reference_markers.fasta -out GCF_900079995.3_ASM90007999v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:50,474] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:50,477] [INFO] Selected 15 target genomes.
[2024-01-25 18:46:50,478] [INFO] Target genome list was writen to GCF_900079995.3_ASM90007999v3_genomic.fna/target_genomes.txt
[2024-01-25 18:46:50,501] [INFO] Task started: fastANI
[2024-01-25 18:46:50,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg049df084-a0ed-469f-8fb6-48321370330f/GCF_900079995.3_ASM90007999v3_genomic.fna.gz --refList GCF_900079995.3_ASM90007999v3_genomic.fna/target_genomes.txt --output GCF_900079995.3_ASM90007999v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:07,377] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:07,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb7c20dd-148b-4252-b4b0-dd843bb5e9b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:07,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb7c20dd-148b-4252-b4b0-dd843bb5e9b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:07,388] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:07,389] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:07,389] [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	100.0	1745	1748	95	conclusive
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	94.2626	1460	1748	95	below_threshold
Citrobacter braakii	strain=ATCC 51113	GCA_002075345.1	57706	57706	type	True	93.3515	1373	1748	95	below_threshold
Citrobacter braakii	strain=FDAARGOS 1421	GCA_019048805.1	57706	57706	type	True	93.3011	1400	1748	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	93.0338	1402	1748	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	92.7948	1404	1748	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	92.7812	1418	1748	95	below_threshold
Citrobacter pasteurii	strain=FDAARGOS 1424	GCA_019047765.1	1563222	1563222	type	True	90.045	1336	1748	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.9111	1009	1748	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.8182	1047	1748	95	below_threshold
Escherichia fergusonii	strain=FDAARGOS_1499	GCA_020097475.1	564	564	type	True	82.0646	871	1748	95	below_threshold
Escherichia fergusonii	strain=ATCC 35469T	GCA_000026225.1	564	564	type	True	82.0501	867	1748	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.754	867	1748	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.7072	845	1748	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.4484	869	1748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:07,390] [INFO] DFAST Taxonomy check result was written to GCF_900079995.3_ASM90007999v3_genomic.fna/tc_result.tsv
[2024-01-25 18:47:07,390] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:07,391] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:07,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb7c20dd-148b-4252-b4b0-dd843bb5e9b8/dqc_reference/checkm_data
[2024-01-25 18:47:07,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:07,442] [INFO] Task started: CheckM
[2024-01-25 18:47:07,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900079995.3_ASM90007999v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900079995.3_ASM90007999v3_genomic.fna/checkm_input GCF_900079995.3_ASM90007999v3_genomic.fna/checkm_result
[2024-01-25 18:47:46,180] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:46,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:46,200] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:46,200] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:46,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900079995.3_ASM90007999v3_genomic.fna/markers.fasta)
[2024-01-25 18:47:46,201] [INFO] Task started: Blastn
[2024-01-25 18:47:46,201] [INFO] Running command: blastn -query GCF_900079995.3_ASM90007999v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb7c20dd-148b-4252-b4b0-dd843bb5e9b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900079995.3_ASM90007999v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:47,338] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:47,341] [INFO] Selected 10 target genomes.
[2024-01-25 18:47:47,342] [INFO] Target genome list was writen to GCF_900079995.3_ASM90007999v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:47,352] [INFO] Task started: fastANI
[2024-01-25 18:47:47,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg049df084-a0ed-469f-8fb6-48321370330f/GCF_900079995.3_ASM90007999v3_genomic.fna.gz --refList GCF_900079995.3_ASM90007999v3_genomic.fna/target_genomes_gtdb.txt --output GCF_900079995.3_ASM90007999v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:59,140] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:59,147] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:59,148] [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_900079995.3	s__Citrobacter europaeus	100.0	1745	1748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	conclusive
GCF_004353845.1	s__Citrobacter freundii_E	94.2626	1460	1748	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	93.3398	1374	1748	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	93.0338	1402	1748	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	92.7812	1418	1748	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	91.8256	1420	1748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCA_000759755.1	s__Citrobacter werkmanii	91.3599	1385	1748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	96.76	96.01	0.88	0.81	67	-
GCF_000155975.1	s__Citrobacter portucalensis_A	91.104	1371	1748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900759445.1	s__Klebsiella sp900759445	87.483	755	1748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632465.1	s__Xenorhabdus budapestensis	77.7945	116	1748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:59,149] [INFO] GTDB search result was written to GCF_900079995.3_ASM90007999v3_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:59,149] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:59,152] [INFO] DFAST_QC result json was written to GCF_900079995.3_ASM90007999v3_genomic.fna/dqc_result.json
[2024-01-25 18:47:59,152] [INFO] DFAST_QC completed!
[2024-01-25 18:47:59,152] [INFO] Total running time: 0h1m24s