[2024-01-24 12:13:57,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:57,913] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:57,913] [INFO] DQC Reference Directory: /var/lib/cwl/stge919a9bd-64f8-4190-9e8c-d3abed3e4f04/dqc_reference
[2024-01-24 12:13:59,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:59,334] [INFO] Task started: Prodigal
[2024-01-24 12:13:59,335] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c610ba7-2848-4c4f-841e-060954252b1a/GCF_000469035.1_sf7882_v1_genomic.fna.gz | prodigal -d GCF_000469035.1_sf7882_v1_genomic.fna/cds.fna -a GCF_000469035.1_sf7882_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:15,887] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:15,887] [INFO] Task started: HMMsearch
[2024-01-24 12:14:15,888] [INFO] Running command: hmmsearch --tblout GCF_000469035.1_sf7882_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge919a9bd-64f8-4190-9e8c-d3abed3e4f04/dqc_reference/reference_markers.hmm GCF_000469035.1_sf7882_v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:16,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:16,312] [INFO] Found 6/6 markers.
[2024-01-24 12:14:16,369] [INFO] Query marker FASTA was written to GCF_000469035.1_sf7882_v1_genomic.fna/markers.fasta
[2024-01-24 12:14:16,369] [INFO] Task started: Blastn
[2024-01-24 12:14:16,369] [INFO] Running command: blastn -query GCF_000469035.1_sf7882_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge919a9bd-64f8-4190-9e8c-d3abed3e4f04/dqc_reference/reference_markers.fasta -out GCF_000469035.1_sf7882_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:17,266] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:17,270] [INFO] Selected 22 target genomes.
[2024-01-24 12:14:17,270] [INFO] Target genome list was writen to GCF_000469035.1_sf7882_v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:17,278] [INFO] Task started: fastANI
[2024-01-24 12:14:17,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c610ba7-2848-4c4f-841e-060954252b1a/GCF_000469035.1_sf7882_v1_genomic.fna.gz --refList GCF_000469035.1_sf7882_v1_genomic.fna/target_genomes.txt --output GCF_000469035.1_sf7882_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:42,940] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:42,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge919a9bd-64f8-4190-9e8c-d3abed3e4f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:42,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge919a9bd-64f8-4190-9e8c-d3abed3e4f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:42,955] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:42,955] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:42,955] [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
Serratia fonticola	strain=LMG 7882	GCA_000469035.1	47917	47917	suspected-type	True	100.0	1782	1799	95	conclusive
Serratia fonticola	strain=DSM 4576	GCA_001006005.1	47917	47917	suspected-type	True	99.9867	1799	1799	95	conclusive
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	82.7323	930	1799	95	below_threshold
Serratia inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	82.7015	938	1799	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	82.6999	945	1799	95	below_threshold
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	82.6759	936	1799	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	82.4968	934	1799	95	below_threshold
Serratia liquefaciens	strain=ATCC 27592	GCA_000422085.1	614	614	type	True	82.3845	962	1799	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	82.3633	939	1799	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S81_jyu2015	GCA_017298875.1	615	615	suspected-type	True	82.3529	940	1799	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	82.3444	941	1799	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	82.2501	927	1799	95	below_threshold
Serratia grimesii	strain=NCTC11543	GCA_900456935.1	82995	82995	type	True	81.8482	880	1799	95	below_threshold
Serratia grimesii	strain=NBRC 13537	GCA_001590905.1	82995	82995	type	True	81.8472	869	1799	95	below_threshold
Chania multitudinisentens	strain=RB-25	GCA_000568195.1	1639108	1639108	type	True	81.6693	926	1799	95	below_threshold
Chania multitudinisentens	strain=RB-25	GCA_000520015.2	1639108	1639108	type	True	81.569	938	1799	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_003666185.1	929813	929813	type	True	80.9983	749	1799	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.1922	520	1799	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.7841	486	1799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:42,956] [INFO] DFAST Taxonomy check result was written to GCF_000469035.1_sf7882_v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:42,957] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:42,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:42,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge919a9bd-64f8-4190-9e8c-d3abed3e4f04/dqc_reference/checkm_data
[2024-01-24 12:14:42,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:43,014] [INFO] Task started: CheckM
[2024-01-24 12:14:43,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000469035.1_sf7882_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000469035.1_sf7882_v1_genomic.fna/checkm_input GCF_000469035.1_sf7882_v1_genomic.fna/checkm_result
[2024-01-24 12:15:31,666] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:31,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:31,690] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:31,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:31,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000469035.1_sf7882_v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:31,691] [INFO] Task started: Blastn
[2024-01-24 12:15:31,692] [INFO] Running command: blastn -query GCF_000469035.1_sf7882_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge919a9bd-64f8-4190-9e8c-d3abed3e4f04/dqc_reference/reference_markers_gtdb.fasta -out GCF_000469035.1_sf7882_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:32,830] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:32,834] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:32,834] [INFO] Target genome list was writen to GCF_000469035.1_sf7882_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:32,846] [INFO] Task started: fastANI
[2024-01-24 12:15:32,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c610ba7-2848-4c4f-841e-060954252b1a/GCF_000469035.1_sf7882_v1_genomic.fna.gz --refList GCF_000469035.1_sf7882_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000469035.1_sf7882_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:49,383] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:49,397] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:49,398] [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_001006005.1	s__Serratia_A fonticola	99.9867	1799	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	96.10	95.03	0.87	0.81	45	conclusive
GCF_000633355.1	s__Serratia_A sp000633355	90.2039	1421	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715025.1	s__Serratia_A fonticola_A	84.9548	1227	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	4	-
GCF_001976145.1	s__Chania oryzae	83.3936	989	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_003591175.1	s__Serratia inhibens	82.7103	937	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	96.90	95.73	0.88	0.85	4	-
GCF_001590925.1	s__Serratia plymuthica	82.6758	936	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.90	96.52	0.93	0.88	29	-
GCF_013337185.1	s__Serratia proteamaculans_D	82.5978	945	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.78	95.57	0.96	0.91	3	-
GCF_900187015.1	s__Serratia ficaria	82.5804	960	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_016742975.1	s__Serratia nevei	82.4563	839	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCA_012719855.1	s__Serratia liquefaciens_A	82.4465	948	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.92	97.90	0.90	0.89	3	-
GCF_000743355.1	s__Chania sp000743355	82.4337	949	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000422085.1	s__Serratia liquefaciens	82.3794	962	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.63	98.20	0.94	0.91	25	-
GCF_003812745.1	s__Serratia sp003812745	82.31	913	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.8367	N/A	N/A	N/A	N/A	1	-
GCF_009831415.1	s__Yersinia canariae	79.6517	419	1799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:49,399] [INFO] GTDB search result was written to GCF_000469035.1_sf7882_v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:49,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:49,404] [INFO] DFAST_QC result json was written to GCF_000469035.1_sf7882_v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:49,404] [INFO] DFAST_QC completed!
[2024-01-24 12:15:49,404] [INFO] Total running time: 0h1m51s