[2024-01-24 10:47:09,215] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,223] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,223] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fe5c94f-e07f-4b89-befc-4dc1165468ee/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,907] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg51f084e5-27aa-4b1c-9beb-22bdea4513a9/GCF_002980625.1_ASM298062v1_genomic.fna.gz | prodigal -d GCF_002980625.1_ASM298062v1_genomic.fna/cds.fna -a GCF_002980625.1_ASM298062v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:23,715] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:23,716] [INFO] Task started: HMMsearch
[2024-01-24 10:47:23,716] [INFO] Running command: hmmsearch --tblout GCF_002980625.1_ASM298062v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fe5c94f-e07f-4b89-befc-4dc1165468ee/dqc_reference/reference_markers.hmm GCF_002980625.1_ASM298062v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:23,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:23,977] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,015] [INFO] Query marker FASTA was written to GCF_002980625.1_ASM298062v1_genomic.fna/markers.fasta
[2024-01-24 10:47:24,015] [INFO] Task started: Blastn
[2024-01-24 10:47:24,015] [INFO] Running command: blastn -query GCF_002980625.1_ASM298062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fe5c94f-e07f-4b89-befc-4dc1165468ee/dqc_reference/reference_markers.fasta -out GCF_002980625.1_ASM298062v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,060] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,065] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:25,066] [INFO] Target genome list was writen to GCF_002980625.1_ASM298062v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,762] [INFO] Task started: fastANI
[2024-01-24 10:47:25,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg51f084e5-27aa-4b1c-9beb-22bdea4513a9/GCF_002980625.1_ASM298062v1_genomic.fna.gz --refList GCF_002980625.1_ASM298062v1_genomic.fna/target_genomes.txt --output GCF_002980625.1_ASM298062v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:45,819] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:45,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fe5c94f-e07f-4b89-befc-4dc1165468ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:45,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fe5c94f-e07f-4b89-befc-4dc1165468ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:45,840] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:45,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:45,841] [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
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	100.0	1214	1217	95	conclusive
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	91.555	938	1217	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.9573	549	1217	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	80.8242	532	1217	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	80.3865	525	1217	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	80.2855	450	1217	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	80.1693	461	1217	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	80.0958	514	1217	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	80.0142	417	1217	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	79.8134	555	1217	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.8129	503	1217	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.7416	549	1217	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	79.5518	487	1217	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	79.5411	546	1217	95	below_threshold
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	79.5271	421	1217	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	79.4999	426	1217	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	79.4943	486	1217	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.3802	517	1217	95	below_threshold
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	79.3185	389	1217	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.9174	424	1217	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.9055	417	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:45,843] [INFO] DFAST Taxonomy check result was written to GCF_002980625.1_ASM298062v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:45,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:45,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:45,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fe5c94f-e07f-4b89-befc-4dc1165468ee/dqc_reference/checkm_data
[2024-01-24 10:47:45,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:45,883] [INFO] Task started: CheckM
[2024-01-24 10:47:45,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002980625.1_ASM298062v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002980625.1_ASM298062v1_genomic.fna/checkm_input GCF_002980625.1_ASM298062v1_genomic.fna/checkm_result
[2024-01-24 10:48:26,510] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:26,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:26,537] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:26,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:26,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002980625.1_ASM298062v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:26,539] [INFO] Task started: Blastn
[2024-01-24 10:48:26,539] [INFO] Running command: blastn -query GCF_002980625.1_ASM298062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fe5c94f-e07f-4b89-befc-4dc1165468ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_002980625.1_ASM298062v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:28,508] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:28,513] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:28,513] [INFO] Target genome list was writen to GCF_002980625.1_ASM298062v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:28,547] [INFO] Task started: fastANI
[2024-01-24 10:48:28,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg51f084e5-27aa-4b1c-9beb-22bdea4513a9/GCF_002980625.1_ASM298062v1_genomic.fna.gz --refList GCF_002980625.1_ASM298062v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002980625.1_ASM298062v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:42,847] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:42,865] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:42,866] [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_002980625.1	s__Malikia spinosa	100.0	1214	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	97.79	97.60	0.88	0.88	3	conclusive
GCF_002980595.1	s__Malikia granosa	91.538	940	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	82.0573	510	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	81.0019	546	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCF_002837135.1	s__Macromonas bipunctata	80.7392	448	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	80.2561	452	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	80.0845	439	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422365.1	s__Pseudorhodoferax sp001422365	79.7776	573	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
GCF_004363315.1	s__Tepidicella xavieri	79.7521	410	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693755.1	s__Tibeticola sp013693755	79.6429	434	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_003337555.1	s__Pseudorhodoferax soli	79.4844	551	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729605.1	s__Brachymonas sp012729605	79.4251	309	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828915.1	s__Serpentinomonas mccroryi	79.3241	389	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	98.21	97.99	0.96	0.95	3	-
GCF_003574675.1	s__Calidifontimicrobium sediminis	79.1527	447	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Calidifontimicrobium	95.0	96.54	96.54	0.86	0.86	2	-
GCF_000800095.1	s__Rhizobacter sp000800095	79.1008	499	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232985.1	s__JAFAMW01 sp019232985	79.055	315	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFAMW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191995.1	s__Rubrivivax sp016191995	78.7176	426	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:42,895] [INFO] GTDB search result was written to GCF_002980625.1_ASM298062v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:42,897] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:42,905] [INFO] DFAST_QC result json was written to GCF_002980625.1_ASM298062v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:42,905] [INFO] DFAST_QC completed!
[2024-01-24 10:48:42,905] [INFO] Total running time: 0h1m34s