[2024-01-24 13:57:15,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:15,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:15,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg7035d15b-e870-46b7-b786-f3a23057b20a/dqc_reference
[2024-01-24 13:57:17,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,361] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg2644d851-7512-454b-b50e-a08abb3a139e/GCF_000482745.1_ASM48274v1_genomic.fna.gz | prodigal -d GCF_000482745.1_ASM48274v1_genomic.fna/cds.fna -a GCF_000482745.1_ASM48274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:29,872] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:29,872] [INFO] Task started: HMMsearch
[2024-01-24 13:57:29,872] [INFO] Running command: hmmsearch --tblout GCF_000482745.1_ASM48274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7035d15b-e870-46b7-b786-f3a23057b20a/dqc_reference/reference_markers.hmm GCF_000482745.1_ASM48274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:30,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:30,149] [INFO] Found 6/6 markers.
[2024-01-24 13:57:30,184] [INFO] Query marker FASTA was written to GCF_000482745.1_ASM48274v1_genomic.fna/markers.fasta
[2024-01-24 13:57:30,185] [INFO] Task started: Blastn
[2024-01-24 13:57:30,185] [INFO] Running command: blastn -query GCF_000482745.1_ASM48274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7035d15b-e870-46b7-b786-f3a23057b20a/dqc_reference/reference_markers.fasta -out GCF_000482745.1_ASM48274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:30,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:30,796] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:30,797] [INFO] Target genome list was writen to GCF_000482745.1_ASM48274v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:30,804] [INFO] Task started: fastANI
[2024-01-24 13:57:30,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg2644d851-7512-454b-b50e-a08abb3a139e/GCF_000482745.1_ASM48274v1_genomic.fna.gz --refList GCF_000482745.1_ASM48274v1_genomic.fna/target_genomes.txt --output GCF_000482745.1_ASM48274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:43,870] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:43,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7035d15b-e870-46b7-b786-f3a23057b20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:43,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7035d15b-e870-46b7-b786-f3a23057b20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:43,885] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:43,885] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:43,885] [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
Oleidesulfovibrio alaskensis	strain=DSM 16109	GCA_000482745.1	58180	58180	type	True	100.0	1171	1173	95	conclusive
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.4387	210	1173	95	below_threshold
Desulfovibrio subterraneus	strain=HN2	GCA_013340285.1	2718620	2718620	type	True	77.3639	208	1173	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.2724	190	1173	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.1801	178	1173	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	77.1577	157	1173	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.1523	161	1173	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.0775	85	1173	95	below_threshold
Desulfovibrio psychrotolerans	strain=JS1	GCA_013340305.1	415242	415242	type	True	76.9374	232	1173	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	76.4603	75	1173	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	76.4398	51	1173	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	76.3937	71	1173	95	below_threshold
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	76.121	76	1173	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	76.0383	63	1173	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	75.7987	51	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:43,887] [INFO] DFAST Taxonomy check result was written to GCF_000482745.1_ASM48274v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:43,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:43,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:43,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7035d15b-e870-46b7-b786-f3a23057b20a/dqc_reference/checkm_data
[2024-01-24 13:57:43,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:43,930] [INFO] Task started: CheckM
[2024-01-24 13:57:43,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000482745.1_ASM48274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000482745.1_ASM48274v1_genomic.fna/checkm_input GCF_000482745.1_ASM48274v1_genomic.fna/checkm_result
[2024-01-24 13:58:23,687] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:23,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:23,704] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:23,705] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:23,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000482745.1_ASM48274v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:23,706] [INFO] Task started: Blastn
[2024-01-24 13:58:23,706] [INFO] Running command: blastn -query GCF_000482745.1_ASM48274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7035d15b-e870-46b7-b786-f3a23057b20a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000482745.1_ASM48274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,603] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,608] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:24,608] [INFO] Target genome list was writen to GCF_000482745.1_ASM48274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:24,633] [INFO] Task started: fastANI
[2024-01-24 13:58:24,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg2644d851-7512-454b-b50e-a08abb3a139e/GCF_000482745.1_ASM48274v1_genomic.fna.gz --refList GCF_000482745.1_ASM48274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000482745.1_ASM48274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:39,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:39,566] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:39,566] [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_000482745.1	s__Oleidesulfovibrio alaskensis	100.0	1171	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Oleidesulfovibrio	95.0	99.29	99.19	0.96	0.95	4	conclusive
GCF_000504305.1	s__Cupidesulfovibrio termitidis	77.4518	209	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	98.21	98.21	0.92	0.92	2	-
GCF_013340285.1	s__Halodesulfovibrio subterraneus	77.373	208	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252375.1	s__Halodesulfovibrio sp003252375	77.2528	188	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195755.1	s__Nitratidesulfovibrio vulgaris	77.1593	159	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Nitratidesulfovibrio	95.0	99.25	98.85	0.97	0.94	6	-
GCF_000226255.1	s__Cupidesulfovibrio sp000226255	76.9684	221	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	96.66	96.06	0.89	0.84	6	-
GCF_013340305.1	s__Halodesulfovibrio psychrotolerans	76.9491	230	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002237645.1	s__Desulfovibrio sp002237645	76.8122	94	1173	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_015062205.1	s__Desulfovibrio desulfuricans_D	76.7299	85	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701705.1	s__Bilophila wadsworthia	76.4028	72	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.41	97.08	0.87	0.83	9	-
GCF_004135975.1	s__Solidesulfovibrio carbinolicus	76.1224	76	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799475.1	s__Humidesulfovibrio sp001799475	76.0189	50	1173	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:39,568] [INFO] GTDB search result was written to GCF_000482745.1_ASM48274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:39,570] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:39,574] [INFO] DFAST_QC result json was written to GCF_000482745.1_ASM48274v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:39,574] [INFO] DFAST_QC completed!
[2024-01-24 13:58:39,574] [INFO] Total running time: 0h1m24s