[2023-06-08 12:32:13,532] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:32:13,534] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:32:13,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg46e9b578-d344-4272-8232-23bb2a13f2de/dqc_reference
[2023-06-08 12:32:14,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:32:14,758] [INFO] Task started: Prodigal
[2023-06-08 12:32:14,758] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4e40f7b-a719-4cfb-8ce8-4348410aa83a/GCA_945876565.1_MiE-22jul19-47_genomic.fna.gz | prodigal -d GCA_945876565.1_MiE-22jul19-47_genomic.fna/cds.fna -a GCA_945876565.1_MiE-22jul19-47_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:32:23,599] [INFO] Task succeeded: Prodigal
[2023-06-08 12:32:23,600] [INFO] Task started: HMMsearch
[2023-06-08 12:32:23,600] [INFO] Running command: hmmsearch --tblout GCA_945876565.1_MiE-22jul19-47_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46e9b578-d344-4272-8232-23bb2a13f2de/dqc_reference/reference_markers.hmm GCA_945876565.1_MiE-22jul19-47_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:32:23,864] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:32:23,865] [INFO] Found 6/6 markers.
[2023-06-08 12:32:23,893] [INFO] Query marker FASTA was written to GCA_945876565.1_MiE-22jul19-47_genomic.fna/markers.fasta
[2023-06-08 12:32:23,893] [INFO] Task started: Blastn
[2023-06-08 12:32:23,893] [INFO] Running command: blastn -query GCA_945876565.1_MiE-22jul19-47_genomic.fna/markers.fasta -db /var/lib/cwl/stg46e9b578-d344-4272-8232-23bb2a13f2de/dqc_reference/reference_markers.fasta -out GCA_945876565.1_MiE-22jul19-47_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:32:24,656] [INFO] Task succeeded: Blastn
[2023-06-08 12:32:24,661] [INFO] Selected 32 target genomes.
[2023-06-08 12:32:24,661] [INFO] Target genome list was writen to GCA_945876565.1_MiE-22jul19-47_genomic.fna/target_genomes.txt
[2023-06-08 12:32:24,667] [INFO] Task started: fastANI
[2023-06-08 12:32:24,668] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e40f7b-a719-4cfb-8ce8-4348410aa83a/GCA_945876565.1_MiE-22jul19-47_genomic.fna.gz --refList GCA_945876565.1_MiE-22jul19-47_genomic.fna/target_genomes.txt --output GCA_945876565.1_MiE-22jul19-47_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:32:45,000] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:45,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46e9b578-d344-4272-8232-23bb2a13f2de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:32:45,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46e9b578-d344-4272-8232-23bb2a13f2de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:32:45,019] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:32:45,019] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:32:45,020] [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
Orrella marina	strain=HZ20	GCA_003058465.1	2163011	2163011	type	True	76.4596	89	893	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.437	67	893	95	below_threshold
Bordetella bronchialis	strain=AU3182	GCA_001676705.1	463025	463025	type	True	76.3898	59	893	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	76.3325	67	893	95	below_threshold
Achromobacter animicus	strain=LMG 26690	GCA_902859585.1	1389935	1389935	type	True	76.2825	60	893	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	76.2739	57	893	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	76.2392	75	893	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	76.2237	57	893	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	76.2146	60	893	95	below_threshold
Achromobacter insolitus	strain=LMG 6003	GCA_002209555.1	217204	217204	type	True	76.1637	61	893	95	below_threshold
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	76.1637	61	893	95	below_threshold
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	76.1346	61	893	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:32:45,022] [INFO] DFAST Taxonomy check result was written to GCA_945876565.1_MiE-22jul19-47_genomic.fna/tc_result.tsv
[2023-06-08 12:32:45,022] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:32:45,022] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:32:45,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46e9b578-d344-4272-8232-23bb2a13f2de/dqc_reference/checkm_data
[2023-06-08 12:32:45,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:32:45,058] [INFO] Task started: CheckM
[2023-06-08 12:32:45,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945876565.1_MiE-22jul19-47_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945876565.1_MiE-22jul19-47_genomic.fna/checkm_input GCA_945876565.1_MiE-22jul19-47_genomic.fna/checkm_result
[2023-06-08 12:33:16,445] [INFO] Task succeeded: CheckM
[2023-06-08 12:33:16,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:33:16,466] [INFO] ===== Completeness check finished =====
[2023-06-08 12:33:16,466] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:33:16,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945876565.1_MiE-22jul19-47_genomic.fna/markers.fasta)
[2023-06-08 12:33:16,467] [INFO] Task started: Blastn
[2023-06-08 12:33:16,467] [INFO] Running command: blastn -query GCA_945876565.1_MiE-22jul19-47_genomic.fna/markers.fasta -db /var/lib/cwl/stg46e9b578-d344-4272-8232-23bb2a13f2de/dqc_reference/reference_markers_gtdb.fasta -out GCA_945876565.1_MiE-22jul19-47_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:33:17,767] [INFO] Task succeeded: Blastn
[2023-06-08 12:33:17,772] [INFO] Selected 32 target genomes.
[2023-06-08 12:33:17,773] [INFO] Target genome list was writen to GCA_945876565.1_MiE-22jul19-47_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:33:17,786] [INFO] Task started: fastANI
[2023-06-08 12:33:17,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e40f7b-a719-4cfb-8ce8-4348410aa83a/GCA_945876565.1_MiE-22jul19-47_genomic.fna.gz --refList GCA_945876565.1_MiE-22jul19-47_genomic.fna/target_genomes_gtdb.txt --output GCA_945876565.1_MiE-22jul19-47_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:33:40,615] [INFO] Task succeeded: fastANI
[2023-06-08 12:33:40,636] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:33:40,636] [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
GCA_007116135.1	s__Algicoccus sp007116135	77.0905	145	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Algicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119665.1	s__Bordetella_B sp002119665	76.5064	62	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067205.1	s__Bordetella_A petrii	76.4652	62	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058465.1	s__Algicoccus marinus	76.4596	89	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Algicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013116765.2	s__Achromobacter deleyi_A	76.4338	55	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009763255.1	s__Bordetella_A sp009763255	76.3946	61	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	97.90	97.90	0.93	0.93	2	-
GCF_001676705.1	s__Bordetella_C bronchialis	76.3898	59	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	99.23	99.23	0.97	0.97	2	-
GCF_002119685.1	s__Bordetella_C sp002119685	76.3814	59	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000657795.2	s__Bordetella pseudohinzii	76.3325	67	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.97	99.86	0.99	0.98	8	-
GCF_002261425.1	s__Bordetella_C sp002261425	76.2386	65	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600685.1	s__Achromobacter spanius_B	76.1886	78	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.56	98.20	0.94	0.92	5	-
GCF_002209555.1	s__Achromobacter insolitus	76.1637	61	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.13	98.86	0.96	0.89	17	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	76.1584	61	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.34	96.34	0.92	0.92	2	-
GCF_002885955.2	s__Achromobacter pulmonis_A	76.1289	66	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_017745595.1	s__Bordetella_A petrii_C	75.9554	78	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192695.1	s__Achromobacter xylosoxidans_C	75.8989	67	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.40	98.40	0.91	0.91	2	-
GCF_009857885.1	s__Pusillimonas_B sp009857885	75.5072	50	893	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:33:40,639] [INFO] GTDB search result was written to GCA_945876565.1_MiE-22jul19-47_genomic.fna/result_gtdb.tsv
[2023-06-08 12:33:40,639] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:33:40,643] [INFO] DFAST_QC result json was written to GCA_945876565.1_MiE-22jul19-47_genomic.fna/dqc_result.json
[2023-06-08 12:33:40,643] [INFO] DFAST_QC completed!
[2023-06-08 12:33:40,643] [INFO] Total running time: 0h1m27s