[2023-06-17 08:06:56,711] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:06:56,716] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:06:56,716] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd803b5a-0bf8-4aae-90b3-011e0ea93fcc/dqc_reference
[2023-06-17 08:06:59,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:06:59,533] [INFO] Task started: Prodigal
[2023-06-17 08:06:59,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e4de2bb-a13e-4f95-861d-4afb4bb1fb20/GCA_028689015.1_ASM2868901v1_genomic.fna.gz | prodigal -d GCA_028689015.1_ASM2868901v1_genomic.fna/cds.fna -a GCA_028689015.1_ASM2868901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:07:08,347] [INFO] Task succeeded: Prodigal
[2023-06-17 08:07:08,348] [INFO] Task started: HMMsearch
[2023-06-17 08:07:08,348] [INFO] Running command: hmmsearch --tblout GCA_028689015.1_ASM2868901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd803b5a-0bf8-4aae-90b3-011e0ea93fcc/dqc_reference/reference_markers.hmm GCA_028689015.1_ASM2868901v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:07:08,621] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:07:08,623] [INFO] Found 6/6 markers.
[2023-06-17 08:07:08,655] [INFO] Query marker FASTA was written to GCA_028689015.1_ASM2868901v1_genomic.fna/markers.fasta
[2023-06-17 08:07:08,656] [INFO] Task started: Blastn
[2023-06-17 08:07:08,656] [INFO] Running command: blastn -query GCA_028689015.1_ASM2868901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd803b5a-0bf8-4aae-90b3-011e0ea93fcc/dqc_reference/reference_markers.fasta -out GCA_028689015.1_ASM2868901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:07:09,491] [INFO] Task succeeded: Blastn
[2023-06-17 08:07:09,497] [INFO] Selected 18 target genomes.
[2023-06-17 08:07:09,497] [INFO] Target genome list was writen to GCA_028689015.1_ASM2868901v1_genomic.fna/target_genomes.txt
[2023-06-17 08:07:09,535] [INFO] Task started: fastANI
[2023-06-17 08:07:09,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e4de2bb-a13e-4f95-861d-4afb4bb1fb20/GCA_028689015.1_ASM2868901v1_genomic.fna.gz --refList GCA_028689015.1_ASM2868901v1_genomic.fna/target_genomes.txt --output GCA_028689015.1_ASM2868901v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:07:23,001] [INFO] Task succeeded: fastANI
[2023-06-17 08:07:23,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd803b5a-0bf8-4aae-90b3-011e0ea93fcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:07:23,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd803b5a-0bf8-4aae-90b3-011e0ea93fcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:07:23,024] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:07:23,024] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 08:07:23,025] [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
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	81.0315	490	913	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	80.9612	481	913	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	80.6472	485	913	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	80.591	489	913	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	77.8553	165	913	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	77.5376	240	913	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.5336	240	913	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.2714	165	913	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.238	162	913	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	77.1414	182	913	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.1353	210	913	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.0838	167	913	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	76.8416	139	913	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	76.4706	117	913	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.4311	122	913	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.2065	112	913	95	below_threshold
Chitinimonas arctica	strain=R3-44	GCA_007431345.1	2594795	2594795	type	True	76.1813	73	913	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	76.1236	107	913	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 08:07:23,027] [INFO] DFAST Taxonomy check result was written to GCA_028689015.1_ASM2868901v1_genomic.fna/tc_result.tsv
[2023-06-17 08:07:23,027] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:07:23,028] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:07:23,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd803b5a-0bf8-4aae-90b3-011e0ea93fcc/dqc_reference/checkm_data
[2023-06-17 08:07:23,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:07:23,062] [INFO] Task started: CheckM
[2023-06-17 08:07:23,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028689015.1_ASM2868901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028689015.1_ASM2868901v1_genomic.fna/checkm_input GCA_028689015.1_ASM2868901v1_genomic.fna/checkm_result
[2023-06-17 08:07:53,236] [INFO] Task succeeded: CheckM
[2023-06-17 08:07:53,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:07:53,261] [INFO] ===== Completeness check finished =====
[2023-06-17 08:07:53,261] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:07:53,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028689015.1_ASM2868901v1_genomic.fna/markers.fasta)
[2023-06-17 08:07:53,265] [INFO] Task started: Blastn
[2023-06-17 08:07:53,266] [INFO] Running command: blastn -query GCA_028689015.1_ASM2868901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd803b5a-0bf8-4aae-90b3-011e0ea93fcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_028689015.1_ASM2868901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:07:54,748] [INFO] Task succeeded: Blastn
[2023-06-17 08:07:54,754] [INFO] Selected 22 target genomes.
[2023-06-17 08:07:54,755] [INFO] Target genome list was writen to GCA_028689015.1_ASM2868901v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:07:54,774] [INFO] Task started: fastANI
[2023-06-17 08:07:54,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e4de2bb-a13e-4f95-861d-4afb4bb1fb20/GCA_028689015.1_ASM2868901v1_genomic.fna.gz --refList GCA_028689015.1_ASM2868901v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028689015.1_ASM2868901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:08:10,048] [INFO] Task succeeded: fastANI
[2023-06-17 08:08:10,066] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 08:08:10,066] [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_001956855.1	s__Azonexus hydrophilus_A	81.3583	516	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429605.1	s__Azonexus hydrophilus	81.0313	490	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.24	97.24	0.86	0.86	2	-
GCF_009469585.1	s__Azonexus sp009469585	80.9821	492	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425245.1	s__Azonexus sp002425245	80.9007	415	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	80.8926	450	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469765.1	s__Azonexus hortensis	80.6551	485	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519045.1	s__Azonexus agitatus	80.5676	481	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
GCA_017983615.1	s__Azonexus sp017983615	80.5509	440	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840765.1	s__Azonexus sp002840765	80.5261	476	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469615.1	s__Azonexus sp009469615	80.4534	445	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440665.1	s__Azonexus sp002440665	80.3998	429	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711155.1	s__Azonexus sp008711155	80.3058	454	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.59	97.59	0.92	0.92	2	-
GCF_000012425.1	s__Azonexus aromaticus_A	80.2754	446	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.34	97.34	0.89	0.89	2	-
GCA_018780195.1	s__Azonexus sp018780195	80.2491	395	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261905.1	s__Azonexus sp018261905	80.2433	457	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379165.1	s__Azonexus sp004379165	80.1965	426	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.95	0.95	2	-
GCA_903922075.1	s__Azonexus sp903922075	80.1167	348	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013363835.1	s__Azonexus sp013363835	80.1135	431	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864195.1	s__Azonexus sp016864195	79.793	444	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003583745.1	s__Azonexus sp003583745	79.7666	443	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930395.1	s__Azonexus sp903930395	79.4463	302	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262285.1	s__UBA1934 sp018262285	76.9451	121	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA1934	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:08:10,069] [INFO] GTDB search result was written to GCA_028689015.1_ASM2868901v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:08:10,069] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:08:10,075] [INFO] DFAST_QC result json was written to GCA_028689015.1_ASM2868901v1_genomic.fna/dqc_result.json
[2023-06-17 08:08:10,075] [INFO] DFAST_QC completed!
[2023-06-17 08:08:10,075] [INFO] Total running time: 0h1m13s