[2023-06-28 12:01:32,397] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:01:32,399] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:01:32,399] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8d8e345-b6a5-4cf6-bbaf-91af62ffaad6/dqc_reference
[2023-06-28 12:01:33,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:01:33,564] [INFO] Task started: Prodigal
[2023-06-28 12:01:33,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg07fa90c8-7f8c-41ac-b2a9-dce1ccb32282/GCA_027442845.1_ASM2744284v1_genomic.fna.gz | prodigal -d GCA_027442845.1_ASM2744284v1_genomic.fna/cds.fna -a GCA_027442845.1_ASM2744284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:01:42,260] [INFO] Task succeeded: Prodigal
[2023-06-28 12:01:42,261] [INFO] Task started: HMMsearch
[2023-06-28 12:01:42,261] [INFO] Running command: hmmsearch --tblout GCA_027442845.1_ASM2744284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8d8e345-b6a5-4cf6-bbaf-91af62ffaad6/dqc_reference/reference_markers.hmm GCA_027442845.1_ASM2744284v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:01:42,473] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:01:42,474] [INFO] Found 6/6 markers.
[2023-06-28 12:01:42,502] [INFO] Query marker FASTA was written to GCA_027442845.1_ASM2744284v1_genomic.fna/markers.fasta
[2023-06-28 12:01:42,503] [INFO] Task started: Blastn
[2023-06-28 12:01:42,503] [INFO] Running command: blastn -query GCA_027442845.1_ASM2744284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8d8e345-b6a5-4cf6-bbaf-91af62ffaad6/dqc_reference/reference_markers.fasta -out GCA_027442845.1_ASM2744284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:43,339] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:43,343] [INFO] Selected 26 target genomes.
[2023-06-28 12:01:43,343] [INFO] Target genome list was writen to GCA_027442845.1_ASM2744284v1_genomic.fna/target_genomes.txt
[2023-06-28 12:01:43,344] [INFO] Task started: fastANI
[2023-06-28 12:01:43,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg07fa90c8-7f8c-41ac-b2a9-dce1ccb32282/GCA_027442845.1_ASM2744284v1_genomic.fna.gz --refList GCA_027442845.1_ASM2744284v1_genomic.fna/target_genomes.txt --output GCA_027442845.1_ASM2744284v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:02:02,955] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:02,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8d8e345-b6a5-4cf6-bbaf-91af62ffaad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:02:02,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8d8e345-b6a5-4cf6-bbaf-91af62ffaad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:02:02,975] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:02:02,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:02:02,975] [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
Thiomonas bhubaneswarensis	strain=DSM 18181	GCA_001517285.1	339866	339866	type	True	79.3838	427	886	95	below_threshold
Thiomonas bhubaneswarensis	strain=DSM 18181	GCA_001418255.1	339866	339866	type	True	79.3606	429	886	95	below_threshold
Thiomonas intermedia	strain=ATCC 15466	GCA_002028405.1	926	926	type	True	79.1695	408	886	95	below_threshold
Thiomonas arsenitoxydans	strain=3As	GCA_000253115.1	426114	426114	type	True	79.0776	442	886	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	77.9843	305	886	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	77.915	276	886	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.8384	286	886	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	77.7097	262	886	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	77.5739	322	886	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	77.5278	281	886	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	77.4996	284	886	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	77.4615	295	886	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	77.4038	256	886	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.3894	234	886	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	77.3857	287	886	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.3628	234	886	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	77.3378	177	886	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	76.9319	223	886	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	76.9084	172	886	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	76.8987	184	886	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	76.8883	196	886	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	76.8871	198	886	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.8553	216	886	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	76.8153	205	886	95	below_threshold
Derxia gummosa	strain=DSM 723	GCA_000482785.1	203699	203699	type	True	76.6858	245	886	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	76.4723	164	886	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:02:02,978] [INFO] DFAST Taxonomy check result was written to GCA_027442845.1_ASM2744284v1_genomic.fna/tc_result.tsv
[2023-06-28 12:02:02,979] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:02:02,979] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:02:02,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8d8e345-b6a5-4cf6-bbaf-91af62ffaad6/dqc_reference/checkm_data
[2023-06-28 12:02:02,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:02:03,012] [INFO] Task started: CheckM
[2023-06-28 12:02:03,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027442845.1_ASM2744284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027442845.1_ASM2744284v1_genomic.fna/checkm_input GCA_027442845.1_ASM2744284v1_genomic.fna/checkm_result
[2023-06-28 12:02:36,252] [INFO] Task succeeded: CheckM
[2023-06-28 12:02:36,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:02:36,273] [INFO] ===== Completeness check finished =====
[2023-06-28 12:02:36,274] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:02:36,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027442845.1_ASM2744284v1_genomic.fna/markers.fasta)
[2023-06-28 12:02:36,274] [INFO] Task started: Blastn
[2023-06-28 12:02:36,274] [INFO] Running command: blastn -query GCA_027442845.1_ASM2744284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8d8e345-b6a5-4cf6-bbaf-91af62ffaad6/dqc_reference/reference_markers_gtdb.fasta -out GCA_027442845.1_ASM2744284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:37,722] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:37,726] [INFO] Selected 13 target genomes.
[2023-06-28 12:02:37,726] [INFO] Target genome list was writen to GCA_027442845.1_ASM2744284v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:02:37,729] [INFO] Task started: fastANI
[2023-06-28 12:02:37,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg07fa90c8-7f8c-41ac-b2a9-dce1ccb32282/GCA_027442845.1_ASM2744284v1_genomic.fna.gz --refList GCA_027442845.1_ASM2744284v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027442845.1_ASM2744284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:02:47,955] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:47,967] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:02:47,968] [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_900088825.1	s__Thiomonas delicata	98.7993	792	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	98.68	98.60	0.90	0.88	3	conclusive
GCF_900089495.1	s__Thiomonas sp900089495	83.2089	666	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044035.1	s__Thiomonas sp013044035	81.523	560	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377645.1	s__Thiomonas sp000377645	80.2047	489	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	96.94	96.87	0.91	0.90	3	-
GCF_001418255.1	s__Thiomonas bhubaneswarensis	79.4065	425	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000733775.1	s__Thiomonas sp000733775	78.9997	432	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234815.1	s__WAJ17 sp019234815	77.4817	213	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WAJ17	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000876015.1	s__Cupriavidus basilensis_B	77.3951	336	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.55	98.55	0.88	0.88	2	-
GCF_002261345.1	s__Bordetella_A sp002261345	77.2555	224	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_002261335.1	s__Bordetella sp002261335	76.9912	227	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCF_000622895.1	s__AVCC01 sp000622895	76.749	113	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AVCC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261475.1	s__Bordetella sp002261475	76.7404	175	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
GCF_000482785.1	s__Derxia gummosa	76.6761	246	886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Derxia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:02:47,970] [INFO] GTDB search result was written to GCA_027442845.1_ASM2744284v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:02:47,970] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:02:47,974] [INFO] DFAST_QC result json was written to GCA_027442845.1_ASM2744284v1_genomic.fna/dqc_result.json
[2023-06-28 12:02:47,974] [INFO] DFAST_QC completed!
[2023-06-28 12:02:47,975] [INFO] Total running time: 0h1m16s