[2024-01-24 11:50:49,685] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,706] [INFO] DQC Reference Directory: /var/lib/cwl/stgba3f1e10-5ef0-4dff-9873-053c5f51c205/dqc_reference
[2024-01-24 11:50:50,930] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,931] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg25316b40-9ac2-4697-947f-f3b0739d8dc7/GCF_002209565.1_ASM220956v1_genomic.fna.gz | prodigal -d GCF_002209565.1_ASM220956v1_genomic.fna/cds.fna -a GCF_002209565.1_ASM220956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:09,035] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:09,036] [INFO] Task started: HMMsearch
[2024-01-24 11:51:09,036] [INFO] Running command: hmmsearch --tblout GCF_002209565.1_ASM220956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba3f1e10-5ef0-4dff-9873-053c5f51c205/dqc_reference/reference_markers.hmm GCF_002209565.1_ASM220956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:09,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:09,334] [INFO] Found 6/6 markers.
[2024-01-24 11:51:09,385] [INFO] Query marker FASTA was written to GCF_002209565.1_ASM220956v1_genomic.fna/markers.fasta
[2024-01-24 11:51:09,386] [INFO] Task started: Blastn
[2024-01-24 11:51:09,386] [INFO] Running command: blastn -query GCF_002209565.1_ASM220956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba3f1e10-5ef0-4dff-9873-053c5f51c205/dqc_reference/reference_markers.fasta -out GCF_002209565.1_ASM220956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:10,448] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:10,452] [INFO] Selected 19 target genomes.
[2024-01-24 11:51:10,453] [INFO] Target genome list was writen to GCF_002209565.1_ASM220956v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:10,461] [INFO] Task started: fastANI
[2024-01-24 11:51:10,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg25316b40-9ac2-4697-947f-f3b0739d8dc7/GCF_002209565.1_ASM220956v1_genomic.fna.gz --refList GCF_002209565.1_ASM220956v1_genomic.fna/target_genomes.txt --output GCF_002209565.1_ASM220956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:28,607] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:28,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba3f1e10-5ef0-4dff-9873-053c5f51c205/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:28,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba3f1e10-5ef0-4dff-9873-053c5f51c205/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:28,623] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:28,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:28,623] [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
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	100.0	1854	1854	95	conclusive
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	87.5189	1148	1854	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	80.1363	491	1854	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	80.0035	530	1854	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	79.8008	562	1854	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	79.7494	479	1854	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.7323	563	1854	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	79.5644	536	1854	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	79.4444	572	1854	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	79.4106	554	1854	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.3882	652	1854	95	below_threshold
Bordetella parapertussis	strain=NCTC5952	GCA_900445785.1	519	519	suspected-type	True	79.3688	562	1854	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	79.3211	593	1854	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	79.2961	512	1854	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.7197	528	1854	95	below_threshold
Achromobacter aloeverae	strain=AVA-1	GCA_004121055.1	1750518	1750518	type	True	78.6814	505	1854	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.5456	390	1854	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	78.3222	473	1854	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	76.9708	363	1854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:28,625] [INFO] DFAST Taxonomy check result was written to GCF_002209565.1_ASM220956v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:28,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:28,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:28,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba3f1e10-5ef0-4dff-9873-053c5f51c205/dqc_reference/checkm_data
[2024-01-24 11:51:28,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:28,678] [INFO] Task started: CheckM
[2024-01-24 11:51:28,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002209565.1_ASM220956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002209565.1_ASM220956v1_genomic.fna/checkm_input GCF_002209565.1_ASM220956v1_genomic.fna/checkm_result
[2024-01-24 11:52:19,728] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:19,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:19,759] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:19,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:19,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002209565.1_ASM220956v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:19,761] [INFO] Task started: Blastn
[2024-01-24 11:52:19,761] [INFO] Running command: blastn -query GCF_002209565.1_ASM220956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba3f1e10-5ef0-4dff-9873-053c5f51c205/dqc_reference/reference_markers_gtdb.fasta -out GCF_002209565.1_ASM220956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:21,828] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:21,832] [INFO] Selected 16 target genomes.
[2024-01-24 11:52:21,832] [INFO] Target genome list was writen to GCF_002209565.1_ASM220956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:21,844] [INFO] Task started: fastANI
[2024-01-24 11:52:21,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg25316b40-9ac2-4697-947f-f3b0739d8dc7/GCF_002209565.1_ASM220956v1_genomic.fna.gz --refList GCF_002209565.1_ASM220956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002209565.1_ASM220956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:38,249] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:38,262] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:38,263] [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_002209565.1	s__Candidimonas nitroreducens	100.0	1854	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019166065.1	s__Candidimonas humi	87.5126	1149	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203015.1	s__Castellaniella defragrans	80.0451	526	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.06	98.49	0.94	0.90	4	-
GCF_017356245.1	s__Bordetella_A petrii_D	79.7627	641	1854	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_003545815.1	s__Pusillimonas caeni	79.7606	478	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	79.7279	563	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002261345.1	s__Bordetella_A sp002261345	79.7275	611	1854	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_003096595.1	s__Pusillimonas noertemannii	79.6432	484	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	99.25	97.76	0.97	0.91	4	-
GCF_001270295.1	s__Achromobacter sp001270295	79.6193	492	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306945.1	s__Bordetella pertussis	79.5642	536	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_017745595.1	s__Bordetella_A petrii_C	79.407	596	1854	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_007679965.1	s__Bordetella_B sp007679965	79.3829	592	1854	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_004342005.1	s__Paracandidimonas soli	79.3357	401	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paracandidimonas	95.0	98.75	98.75	0.86	0.86	2	-
GCF_002261335.1	s__Bordetella sp002261335	79.3167	576	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCF_019218885.1	s__Bordetella_A sp019218885	78.9529	576	1854	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_002261225.1	s__Bordetella_C sp002261225	78.7872	615	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:38,265] [INFO] GTDB search result was written to GCF_002209565.1_ASM220956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:38,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:38,271] [INFO] DFAST_QC result json was written to GCF_002209565.1_ASM220956v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:38,271] [INFO] DFAST_QC completed!
[2024-01-24 11:52:38,272] [INFO] Total running time: 0h1m49s