[2023-06-19 06:38:34,853] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:38:34,856] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:38:34,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg52d90302-77ca-4329-81b2-d5ecc6a0bdfc/dqc_reference
[2023-06-19 06:38:36,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:38:36,047] [INFO] Task started: Prodigal
[2023-06-19 06:38:36,047] [INFO] Running command: gunzip -c /var/lib/cwl/stge7ce0297-7fa0-4c1c-afcc-c7a47018b13d/GCA_018883265.1_ASM1888326v1_genomic.fna.gz | prodigal -d GCA_018883265.1_ASM1888326v1_genomic.fna/cds.fna -a GCA_018883265.1_ASM1888326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:38:41,287] [INFO] Task succeeded: Prodigal
[2023-06-19 06:38:41,288] [INFO] Task started: HMMsearch
[2023-06-19 06:38:41,288] [INFO] Running command: hmmsearch --tblout GCA_018883265.1_ASM1888326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52d90302-77ca-4329-81b2-d5ecc6a0bdfc/dqc_reference/reference_markers.hmm GCA_018883265.1_ASM1888326v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:38:41,511] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:38:41,513] [INFO] Found 6/6 markers.
[2023-06-19 06:38:41,536] [INFO] Query marker FASTA was written to GCA_018883265.1_ASM1888326v1_genomic.fna/markers.fasta
[2023-06-19 06:38:41,537] [INFO] Task started: Blastn
[2023-06-19 06:38:41,537] [INFO] Running command: blastn -query GCA_018883265.1_ASM1888326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d90302-77ca-4329-81b2-d5ecc6a0bdfc/dqc_reference/reference_markers.fasta -out GCA_018883265.1_ASM1888326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:38:42,288] [INFO] Task succeeded: Blastn
[2023-06-19 06:38:42,292] [INFO] Selected 16 target genomes.
[2023-06-19 06:38:42,292] [INFO] Target genome list was writen to GCA_018883265.1_ASM1888326v1_genomic.fna/target_genomes.txt
[2023-06-19 06:38:42,295] [INFO] Task started: fastANI
[2023-06-19 06:38:42,295] [INFO] Running command: fastANI --query /var/lib/cwl/stge7ce0297-7fa0-4c1c-afcc-c7a47018b13d/GCA_018883265.1_ASM1888326v1_genomic.fna.gz --refList GCA_018883265.1_ASM1888326v1_genomic.fna/target_genomes.txt --output GCA_018883265.1_ASM1888326v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:38:51,460] [INFO] Task succeeded: fastANI
[2023-06-19 06:38:51,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52d90302-77ca-4329-81b2-d5ecc6a0bdfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:38:51,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52d90302-77ca-4329-81b2-d5ecc6a0bdfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:38:51,476] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:38:51,477] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 06:38:51,477] [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
Fluviibacter phosphoraccumulans	strain=SHINM1	GCA_016110345.1	1751046	1751046	type	True	79.862	248	584	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	77.6694	112	584	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	77.6454	103	584	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	77.4908	117	584	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.3747	97	584	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.3637	83	584	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	77.3233	111	584	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	77.3068	75	584	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.0122	78	584	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.9584	78	584	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.924	72	584	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	76.897	92	584	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	76.8968	67	584	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	76.8428	66	584	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.8203	86	584	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	76.7865	73	584	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:38:51,479] [INFO] DFAST Taxonomy check result was written to GCA_018883265.1_ASM1888326v1_genomic.fna/tc_result.tsv
[2023-06-19 06:38:51,479] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:38:51,479] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:38:51,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52d90302-77ca-4329-81b2-d5ecc6a0bdfc/dqc_reference/checkm_data
[2023-06-19 06:38:51,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:38:51,506] [INFO] Task started: CheckM
[2023-06-19 06:38:51,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018883265.1_ASM1888326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018883265.1_ASM1888326v1_genomic.fna/checkm_input GCA_018883265.1_ASM1888326v1_genomic.fna/checkm_result
[2023-06-19 06:39:13,550] [INFO] Task succeeded: CheckM
[2023-06-19 06:39:13,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:39:13,570] [INFO] ===== Completeness check finished =====
[2023-06-19 06:39:13,571] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:39:13,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018883265.1_ASM1888326v1_genomic.fna/markers.fasta)
[2023-06-19 06:39:13,571] [INFO] Task started: Blastn
[2023-06-19 06:39:13,572] [INFO] Running command: blastn -query GCA_018883265.1_ASM1888326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d90302-77ca-4329-81b2-d5ecc6a0bdfc/dqc_reference/reference_markers_gtdb.fasta -out GCA_018883265.1_ASM1888326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:39:14,764] [INFO] Task succeeded: Blastn
[2023-06-19 06:39:14,768] [INFO] Selected 14 target genomes.
[2023-06-19 06:39:14,768] [INFO] Target genome list was writen to GCA_018883265.1_ASM1888326v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:39:14,803] [INFO] Task started: fastANI
[2023-06-19 06:39:14,804] [INFO] Running command: fastANI --query /var/lib/cwl/stge7ce0297-7fa0-4c1c-afcc-c7a47018b13d/GCA_018883265.1_ASM1888326v1_genomic.fna.gz --refList GCA_018883265.1_ASM1888326v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018883265.1_ASM1888326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:39:22,124] [INFO] Task succeeded: fastANI
[2023-06-19 06:39:22,146] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:39:22,146] [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
GCA_018883265.1	s__Fluviibacter sp018883265	100.0	581	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018883385.1	s__Fluviibacter sp018883385	81.4568	246	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016110345.1	s__Fluviibacter phosphoraccumulans	79.8634	249	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	99.06	98.97	0.90	0.90	3	-
GCA_903870055.1	s__Fluviibacter sp903870055	79.1476	225	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	99.89	99.89	0.98	0.98	2	-
GCF_001551835.1	s__Azonexus denitrificans	77.5858	105	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653115.1	s__Rhodocyclus purpureus	77.3994	82	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003441615.1	s__Azonexus sp003441615	77.3081	102	584	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	77.1893	116	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983755.1	s__Azonexus sp017983755	77.1574	82	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709335.1	s__Propionivibrio sp016709335	76.9785	78	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.69	98.69	0.87	0.87	2	-
GCF_000527135.1	s__Methyloversatilis discipulorum	76.8203	86	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	97.77	95.54	0.94	0.88	3	-
GCA_009782025.1	s__Azonexus sp009782025	76.6194	65	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:39:22,148] [INFO] GTDB search result was written to GCA_018883265.1_ASM1888326v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:39:22,149] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:39:22,153] [INFO] DFAST_QC result json was written to GCA_018883265.1_ASM1888326v1_genomic.fna/dqc_result.json
[2023-06-19 06:39:22,153] [INFO] DFAST_QC completed!
[2023-06-19 06:39:22,153] [INFO] Total running time: 0h0m47s