[2024-01-24 13:40:55,448] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f102f7a-db0b-466c-b3e1-63a3b1fd4688/dqc_reference
[2024-01-24 13:40:56,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,630] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,630] [INFO] Running command: gunzip -c /var/lib/cwl/stgb21582ed-60c4-4f42-8e6d-dbb29af73766/GCF_001676705.1_ASM167670v1_genomic.fna.gz | prodigal -d GCF_001676705.1_ASM167670v1_genomic.fna/cds.fna -a GCF_001676705.1_ASM167670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:13,804] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:13,804] [INFO] Task started: HMMsearch
[2024-01-24 13:41:13,804] [INFO] Running command: hmmsearch --tblout GCF_001676705.1_ASM167670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f102f7a-db0b-466c-b3e1-63a3b1fd4688/dqc_reference/reference_markers.hmm GCF_001676705.1_ASM167670v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:14,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:14,209] [INFO] Found 6/6 markers.
[2024-01-24 13:41:14,254] [INFO] Query marker FASTA was written to GCF_001676705.1_ASM167670v1_genomic.fna/markers.fasta
[2024-01-24 13:41:14,254] [INFO] Task started: Blastn
[2024-01-24 13:41:14,254] [INFO] Running command: blastn -query GCF_001676705.1_ASM167670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f102f7a-db0b-466c-b3e1-63a3b1fd4688/dqc_reference/reference_markers.fasta -out GCF_001676705.1_ASM167670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:15,208] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:15,210] [INFO] Selected 24 target genomes.
[2024-01-24 13:41:15,211] [INFO] Target genome list was writen to GCF_001676705.1_ASM167670v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:15,216] [INFO] Task started: fastANI
[2024-01-24 13:41:15,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgb21582ed-60c4-4f42-8e6d-dbb29af73766/GCF_001676705.1_ASM167670v1_genomic.fna.gz --refList GCF_001676705.1_ASM167670v1_genomic.fna/target_genomes.txt --output GCF_001676705.1_ASM167670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:41,827] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:41,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f102f7a-db0b-466c-b3e1-63a3b1fd4688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:41,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f102f7a-db0b-466c-b3e1-63a3b1fd4688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:41,841] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:41,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:41,841] [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 bronchialis	strain=AU3182	GCA_001676705.1	463025	463025	type	True	100.0	1958	1959	95	conclusive
Bordetella flabilis	strain=AU10664	GCA_001676725.1	463014	463014	type	True	82.2035	1271	1959	95	below_threshold
Achromobacter aloeverae	strain=AVA-1	GCA_004121055.1	1750518	1750518	type	True	81.0303	1007	1959	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	80.6383	881	1959	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	80.4709	879	1959	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	80.4608	895	1959	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	80.4341	692	1959	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	80.3918	727	1959	95	below_threshold
Bordetella parapertussis	strain=NCTC5952	GCA_900445785.1	519	519	suspected-type	True	80.3651	735	1959	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	80.3302	854	1959	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	80.3206	855	1959	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	80.3201	899	1959	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	80.2888	750	1959	95	below_threshold
Achromobacter aegrifaciens	strain=LMG 26852	GCA_902859735.1	1287736	1287736	type	True	80.2505	861	1959	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	80.2133	726	1959	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	80.1838	696	1959	95	below_threshold
Achromobacter animicus	strain=LMG 26690	GCA_902859585.1	1389935	1389935	type	True	80.1732	752	1959	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	80.1068	866	1959	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	79.8158	769	1959	95	below_threshold
Bordetella holmesii	strain=NCTC12912	GCA_900445775.1	35814	35814	type	True	78.8428	426	1959	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	78.4462	487	1959	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	78.4122	495	1959	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.5001	267	1959	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	76.6911	414	1959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:41,843] [INFO] DFAST Taxonomy check result was written to GCF_001676705.1_ASM167670v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:41,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:41,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:41,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f102f7a-db0b-466c-b3e1-63a3b1fd4688/dqc_reference/checkm_data
[2024-01-24 13:41:41,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:41,898] [INFO] Task started: CheckM
[2024-01-24 13:41:41,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001676705.1_ASM167670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001676705.1_ASM167670v1_genomic.fna/checkm_input GCF_001676705.1_ASM167670v1_genomic.fna/checkm_result
[2024-01-24 13:42:38,406] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:38,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:38,422] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:38,423] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:38,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001676705.1_ASM167670v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:38,423] [INFO] Task started: Blastn
[2024-01-24 13:42:38,423] [INFO] Running command: blastn -query GCF_001676705.1_ASM167670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f102f7a-db0b-466c-b3e1-63a3b1fd4688/dqc_reference/reference_markers_gtdb.fasta -out GCF_001676705.1_ASM167670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:40,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:40,295] [INFO] Selected 8 target genomes.
[2024-01-24 13:42:40,295] [INFO] Target genome list was writen to GCF_001676705.1_ASM167670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:40,315] [INFO] Task started: fastANI
[2024-01-24 13:42:40,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgb21582ed-60c4-4f42-8e6d-dbb29af73766/GCF_001676705.1_ASM167670v1_genomic.fna.gz --refList GCF_001676705.1_ASM167670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001676705.1_ASM167670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:52,247] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:52,254] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:52,254] [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_001676705.1	s__Bordetella_C bronchialis	100.0	1959	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	99.23	99.23	0.97	0.97	2	conclusive
GCF_001704295.1	s__Bordetella_C sp001704295	84.7748	1394	1959	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_002261425.1	s__Bordetella_C sp002261425	84.6612	1458	1959	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_002119685.1	s__Bordetella_C sp002119685	84.3998	1450	1959	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_002261215.1	s__Bordetella_C sp002261215	84.2859	1484	1959	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_002119725.1	s__Bordetella_C sp002119725	82.2821	1053	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	98.76	98.76	0.96	0.96	2	-
GCF_001676725.1	s__Bordetella_C flabilis	82.1817	1272	1959	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_002209485.1	s__Bordetella_C sp002209485	80.4621	989	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:52,255] [INFO] GTDB search result was written to GCF_001676705.1_ASM167670v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:52,256] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:52,259] [INFO] DFAST_QC result json was written to GCF_001676705.1_ASM167670v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:52,259] [INFO] DFAST_QC completed!
[2024-01-24 13:42:52,259] [INFO] Total running time: 0h1m57s