[2024-01-24 12:13:41,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:41,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:41,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bb60dc0-105f-4380-a8ad-ac9c2af735be/dqc_reference
[2024-01-24 12:13:42,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:42,417] [INFO] Task started: Prodigal
[2024-01-24 12:13:42,417] [INFO] Running command: gunzip -c /var/lib/cwl/stgad748588-1215-4436-9363-8bf60e2c202d/GCF_007558815.1_ASM755881v1_genomic.fna.gz | prodigal -d GCF_007558815.1_ASM755881v1_genomic.fna/cds.fna -a GCF_007558815.1_ASM755881v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:00,896] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:00,897] [INFO] Task started: HMMsearch
[2024-01-24 12:14:00,897] [INFO] Running command: hmmsearch --tblout GCF_007558815.1_ASM755881v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bb60dc0-105f-4380-a8ad-ac9c2af735be/dqc_reference/reference_markers.hmm GCF_007558815.1_ASM755881v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:01,263] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:01,264] [INFO] Found 6/6 markers.
[2024-01-24 12:14:01,315] [INFO] Query marker FASTA was written to GCF_007558815.1_ASM755881v1_genomic.fna/markers.fasta
[2024-01-24 12:14:01,315] [INFO] Task started: Blastn
[2024-01-24 12:14:01,315] [INFO] Running command: blastn -query GCF_007558815.1_ASM755881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bb60dc0-105f-4380-a8ad-ac9c2af735be/dqc_reference/reference_markers.fasta -out GCF_007558815.1_ASM755881v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:02,397] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:02,401] [INFO] Selected 22 target genomes.
[2024-01-24 12:14:02,402] [INFO] Target genome list was writen to GCF_007558815.1_ASM755881v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:02,411] [INFO] Task started: fastANI
[2024-01-24 12:14:02,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgad748588-1215-4436-9363-8bf60e2c202d/GCF_007558815.1_ASM755881v1_genomic.fna.gz --refList GCF_007558815.1_ASM755881v1_genomic.fna/target_genomes.txt --output GCF_007558815.1_ASM755881v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:28,405] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:28,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bb60dc0-105f-4380-a8ad-ac9c2af735be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:28,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bb60dc0-105f-4380-a8ad-ac9c2af735be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:28,423] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:28,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:28,424] [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
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	100.0	1969	1977	95	conclusive
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	79.0136	509	1977	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	78.8443	656	1977	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	78.7984	646	1977	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.7801	661	1977	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	78.7782	642	1977	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	78.7724	658	1977	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	78.7717	440	1977	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	78.7584	564	1977	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	78.7333	569	1977	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	78.7144	672	1977	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	78.5294	479	1977	95	below_threshold
Achromobacter aegrifaciens	strain=LMG 26852	GCA_902859735.1	1287736	1287736	type	True	78.4668	587	1977	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	78.4438	600	1977	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	78.344	662	1977	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	78.2836	609	1977	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	78.2822	652	1977	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	78.2383	651	1977	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	78.0779	415	1977	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.5196	437	1977	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.4357	430	1977	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7083	543	1977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:28,426] [INFO] DFAST Taxonomy check result was written to GCF_007558815.1_ASM755881v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:28,428] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:28,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:28,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bb60dc0-105f-4380-a8ad-ac9c2af735be/dqc_reference/checkm_data
[2024-01-24 12:14:28,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:28,486] [INFO] Task started: CheckM
[2024-01-24 12:14:28,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007558815.1_ASM755881v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007558815.1_ASM755881v1_genomic.fna/checkm_input GCF_007558815.1_ASM755881v1_genomic.fna/checkm_result
[2024-01-24 12:15:33,227] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:33,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:33,250] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:33,250] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:33,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007558815.1_ASM755881v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:33,251] [INFO] Task started: Blastn
[2024-01-24 12:15:33,251] [INFO] Running command: blastn -query GCF_007558815.1_ASM755881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bb60dc0-105f-4380-a8ad-ac9c2af735be/dqc_reference/reference_markers_gtdb.fasta -out GCF_007558815.1_ASM755881v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:35,407] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:35,412] [INFO] Selected 19 target genomes.
[2024-01-24 12:15:35,412] [INFO] Target genome list was writen to GCF_007558815.1_ASM755881v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:35,425] [INFO] Task started: fastANI
[2024-01-24 12:15:35,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgad748588-1215-4436-9363-8bf60e2c202d/GCF_007558815.1_ASM755881v1_genomic.fna.gz --refList GCF_007558815.1_ASM755881v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007558815.1_ASM755881v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:56,886] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:56,913] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:56,913] [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_007558815.1	s__Verticiella sediminum	100.0	1970	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Verticiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018904615.1	s__Verticiella sp018904615	80.3383	736	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Verticiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270295.1	s__Achromobacter sp001270295	79.1922	496	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078705.1	s__Bordetella_B ansorpii_A	78.8686	625	1977	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_900606115.1	s__Pigmentiphaga humi	78.8367	509	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859745.1	s__Achromobacter dolens	78.8226	625	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	99.05	99.03	0.93	0.90	8	-
GCF_002261345.1	s__Bordetella_A sp002261345	78.8213	596	1977	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_902859695.1	s__Achromobacter ruhlandii	78.7431	654	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_002885955.2	s__Achromobacter pulmonis_A	78.7392	650	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_902859645.1	s__Achromobacter insuavis	78.6952	675	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_900078315.1	s__Bordetella_B ansorpii	78.667	635	1977	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_003854895.1	s__Pigmentiphaga sp003854895	78.624	572	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203015.1	s__Castellaniella defragrans	78.5768	473	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.06	98.49	0.94	0.90	4	-
GCF_002188465.1	s__Pigmentiphaga sp002188465	78.5223	512	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002188635.1	s__Pigmentiphaga sp002188635	78.5186	571	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.65	99.31	0.97	0.93	3	-
GCF_004216695.1	s__Pigmentiphaga kullae	78.5087	587	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900496975.1	s__Achromobacter veterisilvae	78.3035	607	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571365.1	s__Achromobacter denitrificans	78.2683	653	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
GCF_019166065.1	s__Candidimonas humi	78.1216	410	1977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:56,915] [INFO] GTDB search result was written to GCF_007558815.1_ASM755881v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:56,916] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:56,922] [INFO] DFAST_QC result json was written to GCF_007558815.1_ASM755881v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:56,923] [INFO] DFAST_QC completed!
[2024-01-24 12:15:56,923] [INFO] Total running time: 0h2m16s