[2024-01-25 18:46:35,699] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:35,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:35,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d0b03e6-9e0c-4d1c-ab93-8d6835a6b2cc/dqc_reference
[2024-01-25 18:46:36,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:36,864] [INFO] Task started: Prodigal
[2024-01-25 18:46:36,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg9038cd88-1f3e-4712-8b6c-e92d3415739f/GCF_001544575.2_ASM154457v2_genomic.fna.gz | prodigal -d GCF_001544575.2_ASM154457v2_genomic.fna/cds.fna -a GCF_001544575.2_ASM154457v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:59,224] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:59,224] [INFO] Task started: HMMsearch
[2024-01-25 18:46:59,224] [INFO] Running command: hmmsearch --tblout GCF_001544575.2_ASM154457v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d0b03e6-9e0c-4d1c-ab93-8d6835a6b2cc/dqc_reference/reference_markers.hmm GCF_001544575.2_ASM154457v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:59,572] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:59,573] [INFO] Found 6/6 markers.
[2024-01-25 18:46:59,634] [INFO] Query marker FASTA was written to GCF_001544575.2_ASM154457v2_genomic.fna/markers.fasta
[2024-01-25 18:46:59,634] [INFO] Task started: Blastn
[2024-01-25 18:46:59,634] [INFO] Running command: blastn -query GCF_001544575.2_ASM154457v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d0b03e6-9e0c-4d1c-ab93-8d6835a6b2cc/dqc_reference/reference_markers.fasta -out GCF_001544575.2_ASM154457v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:00,628] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:00,631] [INFO] Selected 14 target genomes.
[2024-01-25 18:47:00,631] [INFO] Target genome list was writen to GCF_001544575.2_ASM154457v2_genomic.fna/target_genomes.txt
[2024-01-25 18:47:00,641] [INFO] Task started: fastANI
[2024-01-25 18:47:00,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg9038cd88-1f3e-4712-8b6c-e92d3415739f/GCF_001544575.2_ASM154457v2_genomic.fna.gz --refList GCF_001544575.2_ASM154457v2_genomic.fna/target_genomes.txt --output GCF_001544575.2_ASM154457v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:30,399] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:30,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d0b03e6-9e0c-4d1c-ab93-8d6835a6b2cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:30,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d0b03e6-9e0c-4d1c-ab93-8d6835a6b2cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:30,409] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:47:30,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:30,409] [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
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	100.0	2699	2702	95	conclusive
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	99.9879	2696	2702	95	conclusive
Caballeronia catudaia		GCA_001544755.2	1777136	1777136	type	True	90.76	1858	2702	95	below_threshold
Caballeronia arvi		GCA_001544695.2	1777135	1777135	type	True	90.6964	2052	2702	95	below_threshold
Caballeronia calidae		GCA_900044055.2	1777139	1777139	type	True	88.8549	1862	2702	95	below_threshold
Caballeronia novacaledonica	strain=LMG 28615	GCA_900258035.1	1544861	1544861	type	True	88.6618	1698	2702	95	below_threshold
Caballeronia pedi		GCA_001544915.2	1777141	1777141	type	True	88.4998	2035	2702	95	below_threshold
Caballeronia zhejiangensis	strain=OP-1	GCA_000698575.1	871203	871203	type	True	88.2795	1819	2702	95	below_threshold
Caballeronia fortuita		GCA_001544835.2	1777138	1777138	type	True	88.0813	1805	2702	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.3664	1345	2702	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.0281	1149	2702	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	80.894	998	2702	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	80.5639	1068	2702	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	80.4567	1161	2702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:30,412] [INFO] DFAST Taxonomy check result was written to GCF_001544575.2_ASM154457v2_genomic.fna/tc_result.tsv
[2024-01-25 18:47:30,413] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:30,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:30,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d0b03e6-9e0c-4d1c-ab93-8d6835a6b2cc/dqc_reference/checkm_data
[2024-01-25 18:47:30,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:30,488] [INFO] Task started: CheckM
[2024-01-25 18:47:30,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001544575.2_ASM154457v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001544575.2_ASM154457v2_genomic.fna/checkm_input GCF_001544575.2_ASM154457v2_genomic.fna/checkm_result
[2024-01-25 18:48:40,559] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:40,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:40,583] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:40,583] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:40,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001544575.2_ASM154457v2_genomic.fna/markers.fasta)
[2024-01-25 18:48:40,584] [INFO] Task started: Blastn
[2024-01-25 18:48:40,585] [INFO] Running command: blastn -query GCF_001544575.2_ASM154457v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d0b03e6-9e0c-4d1c-ab93-8d6835a6b2cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001544575.2_ASM154457v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:42,619] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:42,622] [INFO] Selected 11 target genomes.
[2024-01-25 18:48:42,622] [INFO] Target genome list was writen to GCF_001544575.2_ASM154457v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:42,633] [INFO] Task started: fastANI
[2024-01-25 18:48:42,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg9038cd88-1f3e-4712-8b6c-e92d3415739f/GCF_001544575.2_ASM154457v2_genomic.fna.gz --refList GCF_001544575.2_ASM154457v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001544575.2_ASM154457v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:08,873] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:08,881] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:08,881] [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_001544575.2	s__Caballeronia cordobensis	100.0	2699	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.18	97.54	0.94	0.91	5	conclusive
GCF_001544755.2	s__Caballeronia catudaia	90.7703	1857	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544695.2	s__Caballeronia arvi	90.6993	2052	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900044055.2	s__Caballeronia calidae	88.8703	1860	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258035.1	s__Caballeronia novacaledonica	88.6593	1698	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544915.2	s__Caballeronia pedi	88.534	2030	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018408855.1	s__Caballeronia sp018408855	88.4869	2045	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.23	98.23	0.88	0.88	2	-
GCA_001580565.1	s__Caballeronia megalochromosomata	88.32	1901	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000698575.1	s__Caballeronia zhejiangensis	88.2708	1820	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.44	99.18	0.93	0.92	4	-
GCF_001544835.2	s__Caballeronia fortuita	88.0755	1806	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545075.1	s__Caballeronia ptereochthonis	87.8196	1742	2702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:08,883] [INFO] GTDB search result was written to GCF_001544575.2_ASM154457v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:08,883] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:08,886] [INFO] DFAST_QC result json was written to GCF_001544575.2_ASM154457v2_genomic.fna/dqc_result.json
[2024-01-25 18:49:08,886] [INFO] DFAST_QC completed!
[2024-01-25 18:49:08,886] [INFO] Total running time: 0h2m33s