[2024-01-24 11:43:41,919] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:41,921] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:41,922] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3587667-779a-4e3a-95f0-a21205a78547/dqc_reference
[2024-01-24 11:43:43,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,336] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg33160b2b-f77d-4117-82f3-007d7e0d7996/GCF_014117215.1_ASM1411721v1_genomic.fna.gz | prodigal -d GCF_014117215.1_ASM1411721v1_genomic.fna/cds.fna -a GCF_014117215.1_ASM1411721v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:58,880] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:58,881] [INFO] Task started: HMMsearch
[2024-01-24 11:43:58,881] [INFO] Running command: hmmsearch --tblout GCF_014117215.1_ASM1411721v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3587667-779a-4e3a-95f0-a21205a78547/dqc_reference/reference_markers.hmm GCF_014117215.1_ASM1411721v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:59,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:59,285] [INFO] Found 6/6 markers.
[2024-01-24 11:43:59,324] [INFO] Query marker FASTA was written to GCF_014117215.1_ASM1411721v1_genomic.fna/markers.fasta
[2024-01-24 11:43:59,325] [INFO] Task started: Blastn
[2024-01-24 11:43:59,325] [INFO] Running command: blastn -query GCF_014117215.1_ASM1411721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3587667-779a-4e3a-95f0-a21205a78547/dqc_reference/reference_markers.fasta -out GCF_014117215.1_ASM1411721v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:00,319] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:00,322] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:00,323] [INFO] Target genome list was writen to GCF_014117215.1_ASM1411721v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:00,337] [INFO] Task started: fastANI
[2024-01-24 11:44:00,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg33160b2b-f77d-4117-82f3-007d7e0d7996/GCF_014117215.1_ASM1411721v1_genomic.fna.gz --refList GCF_014117215.1_ASM1411721v1_genomic.fna/target_genomes.txt --output GCF_014117215.1_ASM1411721v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:21,671] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:21,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3587667-779a-4e3a-95f0-a21205a78547/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:21,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3587667-779a-4e3a-95f0-a21205a78547/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:21,692] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:21,693] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:21,693] [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
Stenotrophomonas tumulicola	strain=JCM 30961	GCA_014117215.1	1685415	1685415	type	True	100.0	1428	1431	95	conclusive
Stenotrophomonas chelatiphaga	strain=DSM 21508	GCA_001431535.1	517011	517011	type	True	86.0471	938	1431	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	85.8091	940	1431	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	84.3749	895	1431	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	84.368	936	1431	95	below_threshold
Stenotrophomonas indicatrix	strain=WS40	GCA_002750975.1	2045451	2045451	type	True	84.2204	928	1431	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	84.1867	904	1431	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	84.0877	949	1431	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	84.0724	875	1431	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	83.5787	868	1431	95	below_threshold
Stenotrophomonas rhizophila	strain=DSM14405	GCA_000661955.1	216778	216778	suspected-type	True	83.5265	930	1431	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	83.3787	884	1431	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	82.3639	459	1431	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	82.3512	756	1431	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.4888	753	1431	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.2937	629	1431	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.658	74	1431	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	75.5541	56	1431	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	75.5331	57	1431	95	below_threshold
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	75.3867	60	1431	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	75.3703	71	1431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:21,694] [INFO] DFAST Taxonomy check result was written to GCF_014117215.1_ASM1411721v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:21,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:21,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:21,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3587667-779a-4e3a-95f0-a21205a78547/dqc_reference/checkm_data
[2024-01-24 11:44:21,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:21,739] [INFO] Task started: CheckM
[2024-01-24 11:44:21,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014117215.1_ASM1411721v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014117215.1_ASM1411721v1_genomic.fna/checkm_input GCF_014117215.1_ASM1411721v1_genomic.fna/checkm_result
[2024-01-24 11:45:17,177] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:17,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,199] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:17,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:17,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014117215.1_ASM1411721v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:17,200] [INFO] Task started: Blastn
[2024-01-24 11:45:17,200] [INFO] Running command: blastn -query GCF_014117215.1_ASM1411721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3587667-779a-4e3a-95f0-a21205a78547/dqc_reference/reference_markers_gtdb.fasta -out GCF_014117215.1_ASM1411721v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:18,678] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:18,681] [INFO] Selected 20 target genomes.
[2024-01-24 11:45:18,682] [INFO] Target genome list was writen to GCF_014117215.1_ASM1411721v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:18,706] [INFO] Task started: fastANI
[2024-01-24 11:45:18,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg33160b2b-f77d-4117-82f3-007d7e0d7996/GCF_014117215.1_ASM1411721v1_genomic.fna.gz --refList GCF_014117215.1_ASM1411721v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014117215.1_ASM1411721v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:38,174] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:38,193] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:38,193] [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_014117215.1	s__Stenotrophomonas tumulicola	100.0	1428	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002836635.1	s__Stenotrophomonas sp002836635	86.1037	939	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.91	95.43	0.91	0.85	8	-
GCF_001431535.1	s__Stenotrophomonas chelatiphaga	86.0344	939	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.00	99.00	0.96	0.96	2	-
GCF_014621775.1	s__Stenotrophomonas sp014621775	84.5854	968	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.53	97.52	0.92	0.91	3	-
GCF_003086695.1	s__Stenotrophomonas sp003086695	84.4296	948	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.24	96.14	0.92	0.90	10	-
GCF_003086775.1	s__Stenotrophomonas sp003086775	84.4266	978	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.05	97.07	0.94	0.87	8	-
GCF_001274595.1	s__Stenotrophomonas maltophilia_AJ	84.4093	946	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.15	96.26	0.91	0.88	10	-
GCF_006974125.1	s__Stenotrophomonas maltophilia_O	84.2415	920	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.85	98.84	0.92	0.90	5	-
GCF_001431665.1	s__Stenotrophomonas maltophilia_K	84.1976	894	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002799155.1	s__Stenotrophomonas maltophilia_R	84.1509	930	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887735.1	s__Stenotrophomonas bentonitica_A	84.1491	941	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.97	97.41	0.91	0.87	8	-
GCF_002893095.1	s__Stenotrophomonas sp002893095	84.0422	884	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.47	97.41	0.90	0.90	3	-
GCF_011761925.1	s__Stenotrophomonas sp011761925	83.6854	861	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013185915.1	s__Stenotrophomonas bentonitica	83.5853	868	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002205165.1	s__Stenotrophomonas maltophilia_N	83.3796	892	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.35	98.01	0.93	0.92	6	-
GCF_013387485.1	s__Stenotrophomonas maltophilia_AA	83.2304	897	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.19	96.54	0.90	0.89	3	-
GCF_003751305.1	s__Stenotrophomonas rhizophila_B	83.1117	881	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003935715.1	s__Stenotrophomonas maltophilia_AH	82.9114	798	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.89	97.89	0.86	0.86	2	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	82.3365	775	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
GCF_003353015.1	s__Xanthomonas arboricola_E	81.006	710	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:38,194] [INFO] GTDB search result was written to GCF_014117215.1_ASM1411721v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:38,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:38,199] [INFO] DFAST_QC result json was written to GCF_014117215.1_ASM1411721v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:38,199] [INFO] DFAST_QC completed!
[2024-01-24 11:45:38,199] [INFO] Total running time: 0h1m56s