[2024-01-24 13:09:33,555] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,557] [INFO] DQC Reference Directory: /var/lib/cwl/stgdae0cc91-3760-4233-bf3a-876ad7ae6489/dqc_reference
[2024-01-24 13:09:34,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:34,845] [INFO] Task started: Prodigal
[2024-01-24 13:09:34,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg53f6c21c-03d6-49d4-af9f-393b1f1cb4e4/GCF_000429285.1_ASM42928v1_genomic.fna.gz | prodigal -d GCF_000429285.1_ASM42928v1_genomic.fna/cds.fna -a GCF_000429285.1_ASM42928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:48,964] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:48,965] [INFO] Task started: HMMsearch
[2024-01-24 13:09:48,965] [INFO] Running command: hmmsearch --tblout GCF_000429285.1_ASM42928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdae0cc91-3760-4233-bf3a-876ad7ae6489/dqc_reference/reference_markers.hmm GCF_000429285.1_ASM42928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:49,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:49,250] [INFO] Found 6/6 markers.
[2024-01-24 13:09:49,281] [INFO] Query marker FASTA was written to GCF_000429285.1_ASM42928v1_genomic.fna/markers.fasta
[2024-01-24 13:09:49,282] [INFO] Task started: Blastn
[2024-01-24 13:09:49,282] [INFO] Running command: blastn -query GCF_000429285.1_ASM42928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdae0cc91-3760-4233-bf3a-876ad7ae6489/dqc_reference/reference_markers.fasta -out GCF_000429285.1_ASM42928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:49,947] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:49,950] [INFO] Selected 14 target genomes.
[2024-01-24 13:09:49,950] [INFO] Target genome list was writen to GCF_000429285.1_ASM42928v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:49,963] [INFO] Task started: fastANI
[2024-01-24 13:09:49,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg53f6c21c-03d6-49d4-af9f-393b1f1cb4e4/GCF_000429285.1_ASM42928v1_genomic.fna.gz --refList GCF_000429285.1_ASM42928v1_genomic.fna/target_genomes.txt --output GCF_000429285.1_ASM42928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:00,611] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:00,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdae0cc91-3760-4233-bf3a-876ad7ae6489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:00,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdae0cc91-3760-4233-bf3a-876ad7ae6489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:00,624] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:00,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:00,624] [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
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	100.0	1206	1215	95	conclusive
Megalodesulfovibrio gigas	strain=ATCC 19364	GCA_000468495.1	879	879	type	True	99.9264	1207	1215	95	conclusive
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	77.4083	278	1215	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.391	255	1215	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.3449	227	1215	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.3167	124	1215	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	77.2867	118	1215	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	77.2764	236	1215	95	below_threshold
Desulfohalovibrio reitneri	strain=L21-Syr-AB	GCA_000711295.1	1307759	1307759	type	True	77.274	239	1215	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.2664	207	1215	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.0401	147	1215	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	76.8814	147	1215	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	76.284	85	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:00,626] [INFO] DFAST Taxonomy check result was written to GCF_000429285.1_ASM42928v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:00,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:00,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:00,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdae0cc91-3760-4233-bf3a-876ad7ae6489/dqc_reference/checkm_data
[2024-01-24 13:10:00,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:00,672] [INFO] Task started: CheckM
[2024-01-24 13:10:00,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429285.1_ASM42928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429285.1_ASM42928v1_genomic.fna/checkm_input GCF_000429285.1_ASM42928v1_genomic.fna/checkm_result
[2024-01-24 13:10:45,750] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:45,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:45,772] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:45,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:45,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429285.1_ASM42928v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:45,774] [INFO] Task started: Blastn
[2024-01-24 13:10:45,774] [INFO] Running command: blastn -query GCF_000429285.1_ASM42928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdae0cc91-3760-4233-bf3a-876ad7ae6489/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429285.1_ASM42928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:46,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:46,826] [INFO] Selected 23 target genomes.
[2024-01-24 13:10:46,827] [INFO] Target genome list was writen to GCF_000429285.1_ASM42928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:46,858] [INFO] Task started: fastANI
[2024-01-24 13:10:46,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg53f6c21c-03d6-49d4-af9f-393b1f1cb4e4/GCF_000429285.1_ASM42928v1_genomic.fna.gz --refList GCF_000429285.1_ASM42928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429285.1_ASM42928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:01,783] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:01,800] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:01,801] [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_000468495.1	s__Megalodesulfovibrio gigas	99.9264	1207	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Megalodesulfovibrio	95.0	99.93	99.93	0.99	0.99	2	conclusive
GCF_013085545.1	s__Desulfovibrio_R marinus	77.8249	320	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio_R	95.0	99.02	99.02	0.95	0.95	2	-
GCF_007625075.1	s__Desulfovibrio_R indonesiensis	77.5772	241	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519125.1	s__Desulfocurvus vexinensis	77.4929	291	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfocurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013019105.1	s__Fundidesulfovibrio sp013019105	77.4343	275	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682075.1	s__Cupidesulfovibrio liaohensis	77.3745	223	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843875.1	s__Desulfovibrio sp900556755	77.3236	137	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	98.27	96.78	0.88	0.81	10	-
GCA_015709205.1	s__JACCQO01 sp015709205	77.2968	283	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__JACCQO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711295.1	s__Desulfohalovibrio reitneri	77.2914	237	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfohalovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422205.1	s__Desulfohalovibrio sp000422205	77.2603	244	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfohalovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002382645.1	s__Aminidesulfovibrio sp002382645	77.2269	228	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Aminidesulfovibrio	95.0	99.05	98.75	0.90	0.87	3	-
GCF_000195755.1	s__Nitratidesulfovibrio vulgaris	77.1968	122	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Nitratidesulfovibrio	95.0	99.25	98.85	0.97	0.94	6	-
GCA_016218665.1	s__Humidesulfovibrio sp016218665	77.1524	201	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799475.1	s__Humidesulfovibrio sp001799475	77.0952	191	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156375.1	s__Desulfovibrio piger	77.0333	148	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	99.18	98.09	0.98	0.96	5	-
GCA_019118345.1	s__Desulfovibrio intestinavium	77.0028	117	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004796465.1	s__MADRE1 sp004796465	76.9581	167	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__MADRE1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696265.1	s__Desulfovibrio porci	76.8664	147	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.64	99.64	0.91	0.91	2	-
GCA_015062205.1	s__Desulfovibrio desulfuricans_D	76.8168	134	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452635.1	s__UBA6814 sp002452635	76.6791	251	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__UBA6814	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900079685.1	s__FLUQ01 sp900079685	76.6289	93	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__FLUQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541395.1	s__Mailhella merdigallinarum	76.0914	92	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	99.42	99.13	0.88	0.80	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:01,802] [INFO] GTDB search result was written to GCF_000429285.1_ASM42928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:01,803] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:01,807] [INFO] DFAST_QC result json was written to GCF_000429285.1_ASM42928v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:01,807] [INFO] DFAST_QC completed!
[2024-01-24 13:11:01,807] [INFO] Total running time: 0h1m28s