[2024-01-24 12:13:23,567] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:23,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:23,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg926ca9a5-d0a6-4617-9969-22c0b78a3027/dqc_reference
[2024-01-24 12:13:24,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:24,847] [INFO] Task started: Prodigal
[2024-01-24 12:13:24,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg809241a3-a3da-41d2-84d6-a2224e4296fb/GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/cds.fna -a GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:40,235] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:40,236] [INFO] Task started: HMMsearch
[2024-01-24 12:13:40,236] [INFO] Running command: hmmsearch --tblout GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg926ca9a5-d0a6-4617-9969-22c0b78a3027/dqc_reference/reference_markers.hmm GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:40,584] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:40,585] [INFO] Found 6/6 markers.
[2024-01-24 12:13:40,625] [INFO] Query marker FASTA was written to GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:40,626] [INFO] Task started: Blastn
[2024-01-24 12:13:40,626] [INFO] Running command: blastn -query GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg926ca9a5-d0a6-4617-9969-22c0b78a3027/dqc_reference/reference_markers.fasta -out GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:41,660] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:41,662] [INFO] Selected 11 target genomes.
[2024-01-24 12:13:41,663] [INFO] Target genome list was writen to GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:41,668] [INFO] Task started: fastANI
[2024-01-24 12:13:41,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg809241a3-a3da-41d2-84d6-a2224e4296fb/GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna.gz --refList GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:54,651] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:54,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg926ca9a5-d0a6-4617-9969-22c0b78a3027/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:54,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg926ca9a5-d0a6-4617-9969-22c0b78a3027/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:54,663] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:54,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:54,664] [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 pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	100.0	1463	1465	95	conclusive
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	98.7187	1310	1465	95	conclusive
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	92.6835	1240	1465	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	91.8428	1238	1465	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	91.783	1231	1465	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	91.696	1155	1465	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.7417	929	1465	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.8872	828	1465	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.3656	501	1465	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.7258	878	1465	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.3262	718	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:54,674] [INFO] DFAST Taxonomy check result was written to GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:13:54,678] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:54,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:54,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg926ca9a5-d0a6-4617-9969-22c0b78a3027/dqc_reference/checkm_data
[2024-01-24 12:13:54,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:54,748] [INFO] Task started: CheckM
[2024-01-24 12:13:54,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/checkm_input GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:14:52,985] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:52,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:53,011] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:53,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:53,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:14:53,012] [INFO] Task started: Blastn
[2024-01-24 12:14:53,012] [INFO] Running command: blastn -query GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg926ca9a5-d0a6-4617-9969-22c0b78a3027/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:55,032] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:55,037] [INFO] Selected 16 target genomes.
[2024-01-24 12:14:55,037] [INFO] Target genome list was writen to GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:55,051] [INFO] Task started: fastANI
[2024-01-24 12:14:55,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg809241a3-a3da-41d2-84d6-a2224e4296fb/GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna.gz --refList GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:16,662] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:16,676] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:16,676] [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_900101175.1	s__Stenotrophomonas pavanii	100.0	1463	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.59	98.08	0.91	0.84	20	conclusive
GCF_000284595.1	s__Stenotrophomonas maltophilia_F	93.8479	1318	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.76	98.38	0.92	0.88	60	-
GCA_014171555.1	s__Stenotrophomonas maltophilia_AK	93.2035	1322	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.10	95.71	0.92	0.85	90	-
GCF_006970445.1	s__Stenotrophomonas maltophilia_AU	92.9216	1295	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002799245.1	s__Stenotrophomonas maltophilia_S	92.609	1268	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192255.1	s__Stenotrophomonas sp002192255	92.563	1295	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.64	95.45	0.89	0.84	9	-
GCF_002799155.1	s__Stenotrophomonas maltophilia_R	92.3212	1283	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382065.1	s__Stenotrophomonas maltophilia_B	92.1561	1304	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.83	97.17	0.91	0.87	24	-
GCF_900186865.1	s__Stenotrophomonas maltophilia	91.826	1300	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.99	97.31	0.92	0.87	234	-
GCF_001431665.1	s__Stenotrophomonas maltophilia_K	91.6813	1219	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001431625.1	s__Stenotrophomonas geniculata	91.5405	1202	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.51	96.26	0.87	0.77	45	-
GCF_002138415.1	s__Stenotrophomonas maltophilia_G	91.5365	1280	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
GCF_006974125.1	s__Stenotrophomonas maltophilia_O	91.416	1259	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.85	98.84	0.92	0.90	5	-
GCF_013464915.1	s__Stenotrophomonas maltophilia_AT	91.2532	1211	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCF_001274595.1	s__Stenotrophomonas maltophilia_AJ	91.0404	1237	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.15	96.26	0.91	0.88	10	-
GCF_003028475.1	s__Stenotrophomonas sp003028475	90.8006	1229	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:16,678] [INFO] GTDB search result was written to GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:16,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:16,682] [INFO] DFAST_QC result json was written to GCF_900101175.1_IMG-taxon_2623620583_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:15:16,682] [INFO] DFAST_QC completed!
[2024-01-24 12:15:16,682] [INFO] Total running time: 0h1m53s