[2023-06-27 05:57:49,231] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:57:49,234] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:57:49,234] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2e755b5-7f6d-46c1-a2a3-69ebf055f1aa/dqc_reference
[2023-06-27 05:57:51,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:57:51,378] [INFO] Task started: Prodigal
[2023-06-27 05:57:51,379] [INFO] Running command: gunzip -c /var/lib/cwl/stg6826d013-87b6-4209-920f-a835fb57e48a/GCA_002294075.1_ASM229407v1_genomic.fna.gz | prodigal -d GCA_002294075.1_ASM229407v1_genomic.fna/cds.fna -a GCA_002294075.1_ASM229407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:58:13,842] [INFO] Task succeeded: Prodigal
[2023-06-27 05:58:13,843] [INFO] Task started: HMMsearch
[2023-06-27 05:58:13,843] [INFO] Running command: hmmsearch --tblout GCA_002294075.1_ASM229407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2e755b5-7f6d-46c1-a2a3-69ebf055f1aa/dqc_reference/reference_markers.hmm GCA_002294075.1_ASM229407v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:58:14,199] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:58:14,201] [INFO] Found 6/6 markers.
[2023-06-27 05:58:14,251] [INFO] Query marker FASTA was written to GCA_002294075.1_ASM229407v1_genomic.fna/markers.fasta
[2023-06-27 05:58:14,251] [INFO] Task started: Blastn
[2023-06-27 05:58:14,251] [INFO] Running command: blastn -query GCA_002294075.1_ASM229407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2e755b5-7f6d-46c1-a2a3-69ebf055f1aa/dqc_reference/reference_markers.fasta -out GCA_002294075.1_ASM229407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:15,355] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:15,360] [INFO] Selected 9 target genomes.
[2023-06-27 05:58:15,361] [INFO] Target genome list was writen to GCA_002294075.1_ASM229407v1_genomic.fna/target_genomes.txt
[2023-06-27 05:58:15,433] [INFO] Task started: fastANI
[2023-06-27 05:58:15,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg6826d013-87b6-4209-920f-a835fb57e48a/GCA_002294075.1_ASM229407v1_genomic.fna.gz --refList GCA_002294075.1_ASM229407v1_genomic.fna/target_genomes.txt --output GCA_002294075.1_ASM229407v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:58:31,481] [INFO] Task succeeded: fastANI
[2023-06-27 05:58:31,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2e755b5-7f6d-46c1-a2a3-69ebf055f1aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:58:31,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2e755b5-7f6d-46c1-a2a3-69ebf055f1aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:58:31,493] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2023-06-27 05:58:31,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 05:58:31,493] [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
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	98.7335	2041	2214	95	conclusive
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	98.7083	2043	2214	95	conclusive
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	98.662	2019	2214	95	conclusive
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	98.6273	2064	2214	95	conclusive
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	92.5479	1749	2214	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	85.069	1426	2214	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	82.9957	879	2214	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.2359	382	2214	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.6422	580	2214	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:58:31,495] [INFO] DFAST Taxonomy check result was written to GCA_002294075.1_ASM229407v1_genomic.fna/tc_result.tsv
[2023-06-27 05:58:31,496] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:58:31,496] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:58:31,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2e755b5-7f6d-46c1-a2a3-69ebf055f1aa/dqc_reference/checkm_data
[2023-06-27 05:58:31,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:58:31,565] [INFO] Task started: CheckM
[2023-06-27 05:58:31,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002294075.1_ASM229407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002294075.1_ASM229407v1_genomic.fna/checkm_input GCA_002294075.1_ASM229407v1_genomic.fna/checkm_result
[2023-06-27 05:59:41,977] [INFO] Task succeeded: CheckM
[2023-06-27 05:59:41,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:59:42,004] [INFO] ===== Completeness check finished =====
[2023-06-27 05:59:42,004] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:59:42,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002294075.1_ASM229407v1_genomic.fna/markers.fasta)
[2023-06-27 05:59:42,005] [INFO] Task started: Blastn
[2023-06-27 05:59:42,005] [INFO] Running command: blastn -query GCA_002294075.1_ASM229407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2e755b5-7f6d-46c1-a2a3-69ebf055f1aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_002294075.1_ASM229407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:59:44,598] [INFO] Task succeeded: Blastn
[2023-06-27 05:59:44,603] [INFO] Selected 6 target genomes.
[2023-06-27 05:59:44,604] [INFO] Target genome list was writen to GCA_002294075.1_ASM229407v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:59:44,613] [INFO] Task started: fastANI
[2023-06-27 05:59:44,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg6826d013-87b6-4209-920f-a835fb57e48a/GCA_002294075.1_ASM229407v1_genomic.fna.gz --refList GCA_002294075.1_ASM229407v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002294075.1_ASM229407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:59:56,841] [INFO] Task succeeded: fastANI
[2023-06-27 05:59:56,853] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:59:56,854] [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_001457475.1	s__Achromobacter xylosoxidans	98.6964	2044	2214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	conclusive
GCF_902859695.1	s__Achromobacter ruhlandii	92.9349	1820	2214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_902859745.1	s__Achromobacter dolens	92.7876	1745	2214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	99.05	99.03	0.93	0.90	8	-
GCF_902859645.1	s__Achromobacter insuavis	92.551	1750	2214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_016127315.1	s__Achromobacter insuavis_A	92.299	1831	2214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_902859765.1	s__Achromobacter pulmonis	91.0412	1580	2214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-27 05:59:56,862] [INFO] GTDB search result was written to GCA_002294075.1_ASM229407v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:59:56,863] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:59:56,881] [INFO] DFAST_QC result json was written to GCA_002294075.1_ASM229407v1_genomic.fna/dqc_result.json
[2023-06-27 05:59:56,881] [INFO] DFAST_QC completed!
[2023-06-27 05:59:56,881] [INFO] Total running time: 0h2m8s