[2024-01-25 18:54:35,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:35,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:35,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg77bb8c7d-174f-42f7-b8c2-393145f1b0ea/dqc_reference
[2024-01-25 18:54:36,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:36,672] [INFO] Task started: Prodigal
[2024-01-25 18:54:36,672] [INFO] Running command: gunzip -c /var/lib/cwl/stgda621efd-a618-4ff5-846e-52e8e3ccf5b6/GCF_000306945.1_ASM30694v1_genomic.fna.gz | prodigal -d GCF_000306945.1_ASM30694v1_genomic.fna/cds.fna -a GCF_000306945.1_ASM30694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:48,415] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:48,415] [INFO] Task started: HMMsearch
[2024-01-25 18:54:48,415] [INFO] Running command: hmmsearch --tblout GCF_000306945.1_ASM30694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77bb8c7d-174f-42f7-b8c2-393145f1b0ea/dqc_reference/reference_markers.hmm GCF_000306945.1_ASM30694v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:48,687] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:48,688] [INFO] Found 6/6 markers.
[2024-01-25 18:54:48,727] [INFO] Query marker FASTA was written to GCF_000306945.1_ASM30694v1_genomic.fna/markers.fasta
[2024-01-25 18:54:48,727] [INFO] Task started: Blastn
[2024-01-25 18:54:48,727] [INFO] Running command: blastn -query GCF_000306945.1_ASM30694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77bb8c7d-174f-42f7-b8c2-393145f1b0ea/dqc_reference/reference_markers.fasta -out GCF_000306945.1_ASM30694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:49,857] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:49,859] [INFO] Selected 12 target genomes.
[2024-01-25 18:54:49,860] [INFO] Target genome list was writen to GCF_000306945.1_ASM30694v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:49,865] [INFO] Task started: fastANI
[2024-01-25 18:54:49,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgda621efd-a618-4ff5-846e-52e8e3ccf5b6/GCF_000306945.1_ASM30694v1_genomic.fna.gz --refList GCF_000306945.1_ASM30694v1_genomic.fna/target_genomes.txt --output GCF_000306945.1_ASM30694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:39,870] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:39,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77bb8c7d-174f-42f7-b8c2-393145f1b0ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:39,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77bb8c7d-174f-42f7-b8c2-393145f1b0ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:39,879] [INFO] Found 12 fastANI hits (8 hits with ANI > threshold)
[2024-01-25 18:55:39,879] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:55:39,879] [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
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	100.0	1344	1347	95	inconclusive
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	99.994	1344	1347	95	inconclusive
Bordetella parapertussis	strain=NCTC5952	GCA_900445785.1	519	519	suspected-type	True	98.3575	1201	1347	95	inconclusive
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	98.3143	1213	1347	95	inconclusive
Bordetella parapertussis	strain=FDAARGOS_177	GCA_001525545.2	519	519	suspected-type	True	98.2793	1228	1347	95	inconclusive
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	98.0933	1232	1347	95	inconclusive
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	98.0504	1163	1347	95	inconclusive
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	97.9871	1127	1347	95	inconclusive
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	83.3793	870	1347	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	81.8041	824	1347	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.7996	320	1347	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.3291	411	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:39,881] [INFO] DFAST Taxonomy check result was written to GCF_000306945.1_ASM30694v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:39,881] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:39,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:39,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77bb8c7d-174f-42f7-b8c2-393145f1b0ea/dqc_reference/checkm_data
[2024-01-25 18:55:39,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:39,926] [INFO] Task started: CheckM
[2024-01-25 18:55:39,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000306945.1_ASM30694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000306945.1_ASM30694v1_genomic.fna/checkm_input GCF_000306945.1_ASM30694v1_genomic.fna/checkm_result
[2024-01-25 18:56:20,336] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:20,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:20,362] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:20,363] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:20,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000306945.1_ASM30694v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:20,364] [INFO] Task started: Blastn
[2024-01-25 18:56:20,364] [INFO] Running command: blastn -query GCF_000306945.1_ASM30694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77bb8c7d-174f-42f7-b8c2-393145f1b0ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_000306945.1_ASM30694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:22,607] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:22,609] [INFO] Selected 20 target genomes.
[2024-01-25 18:56:22,610] [INFO] Target genome list was writen to GCF_000306945.1_ASM30694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:22,627] [INFO] Task started: fastANI
[2024-01-25 18:56:22,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgda621efd-a618-4ff5-846e-52e8e3ccf5b6/GCF_000306945.1_ASM30694v1_genomic.fna.gz --refList GCF_000306945.1_ASM30694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000306945.1_ASM30694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:04,079] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:04,091] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:04,091] [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_000306945.1	s__Bordetella pertussis	100.0	1343	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	conclusive
GCF_016127315.1	s__Achromobacter insuavis_A	83.403	884	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_002885955.2	s__Achromobacter pulmonis_A	83.4005	891	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_002261345.1	s__Bordetella_A sp002261345	83.3799	846	1347	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_001457475.1	s__Achromobacter xylosoxidans	83.3451	868	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
GCF_902859645.1	s__Achromobacter insuavis	83.3328	856	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_017356245.1	s__Bordetella_A petrii_D	83.2952	843	1347	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_902859745.1	s__Achromobacter dolens	83.2467	842	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	99.05	99.03	0.93	0.90	8	-
GCF_002902905.1	s__Achromobacter sp002902905	83.2239	862	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.15	96.15	0.87	0.87	2	-
GCF_902859695.1	s__Achromobacter ruhlandii	83.2207	868	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_002261335.1	s__Bordetella sp002261335	83.1739	875	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCF_001270295.1	s__Achromobacter sp001270295	82.9874	674	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679965.1	s__Bordetella_B sp007679965	82.8019	812	1347	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_014490035.1	s__Achromobacter bronchisepticus_A	82.7649	850	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
GCF_017745595.1	s__Bordetella_A petrii_C	82.7559	786	1347	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_001571365.1	s__Achromobacter denitrificans	82.7019	867	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
GCF_900496975.1	s__Achromobacter veterisilvae	82.7009	866	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859735.1	s__Achromobacter aegrifaciens	82.6254	858	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_002261475.1	s__Bordetella sp002261475	82.2532	820	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
GCF_902859585.1	s__Achromobacter animicus	82.1325	793	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.58	96.10	0.93	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:04,093] [INFO] GTDB search result was written to GCF_000306945.1_ASM30694v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:04,093] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:04,096] [INFO] DFAST_QC result json was written to GCF_000306945.1_ASM30694v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:04,096] [INFO] DFAST_QC completed!
[2024-01-25 18:57:04,096] [INFO] Total running time: 0h2m29s