[2024-01-24 11:34:41,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,393] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ee9f6ab-47ca-46c9-8232-09abbd413962/dqc_reference
[2024-01-24 11:34:42,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,773] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg298e6509-f7ea-4809-a576-c051fa50dd66/GCF_013340285.1_ASM1334028v1_genomic.fna.gz | prodigal -d GCF_013340285.1_ASM1334028v1_genomic.fna/cds.fna -a GCF_013340285.1_ASM1334028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:56,753] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:56,753] [INFO] Task started: HMMsearch
[2024-01-24 11:34:56,753] [INFO] Running command: hmmsearch --tblout GCF_013340285.1_ASM1334028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ee9f6ab-47ca-46c9-8232-09abbd413962/dqc_reference/reference_markers.hmm GCF_013340285.1_ASM1334028v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:57,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:57,039] [INFO] Found 6/6 markers.
[2024-01-24 11:34:57,076] [INFO] Query marker FASTA was written to GCF_013340285.1_ASM1334028v1_genomic.fna/markers.fasta
[2024-01-24 11:34:57,077] [INFO] Task started: Blastn
[2024-01-24 11:34:57,077] [INFO] Running command: blastn -query GCF_013340285.1_ASM1334028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ee9f6ab-47ca-46c9-8232-09abbd413962/dqc_reference/reference_markers.fasta -out GCF_013340285.1_ASM1334028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:57,738] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:57,742] [INFO] Selected 18 target genomes.
[2024-01-24 11:34:57,742] [INFO] Target genome list was writen to GCF_013340285.1_ASM1334028v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:57,749] [INFO] Task started: fastANI
[2024-01-24 11:34:57,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg298e6509-f7ea-4809-a576-c051fa50dd66/GCF_013340285.1_ASM1334028v1_genomic.fna.gz --refList GCF_013340285.1_ASM1334028v1_genomic.fna/target_genomes.txt --output GCF_013340285.1_ASM1334028v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:14,628] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:14,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ee9f6ab-47ca-46c9-8232-09abbd413962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:14,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ee9f6ab-47ca-46c9-8232-09abbd413962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:14,640] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:14,641] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:14,641] [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
Desulfovibrio subterraneus	strain=HN2	GCA_013340285.1	2718620	2718620	type	True	100.0	1366	1366	95	conclusive
Desulfovibrio psychrotolerans	strain=JS1	GCA_013340305.1	415242	415242	type	True	79.6414	628	1366	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.6645	229	1366	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	77.4776	185	1366	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.4627	196	1366	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.4588	271	1366	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.4571	223	1366	95	below_threshold
Oleidesulfovibrio alaskensis	strain=DSM 16109	GCA_000482745.1	58180	58180	type	True	77.4444	201	1366	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.2689	116	1366	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	76.6715	95	1366	95	below_threshold
Desulfobaculum xiamenense	strain=DSM 24233	GCA_011927665.1	995050	995050	type	True	76.5954	130	1366	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	76.4559	89	1366	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	76.2791	119	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:14,642] [INFO] DFAST Taxonomy check result was written to GCF_013340285.1_ASM1334028v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:14,643] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:14,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:14,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ee9f6ab-47ca-46c9-8232-09abbd413962/dqc_reference/checkm_data
[2024-01-24 11:35:14,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:14,688] [INFO] Task started: CheckM
[2024-01-24 11:35:14,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013340285.1_ASM1334028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013340285.1_ASM1334028v1_genomic.fna/checkm_input GCF_013340285.1_ASM1334028v1_genomic.fna/checkm_result
[2024-01-24 11:35:55,570] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:55,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:55,588] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:55,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:55,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013340285.1_ASM1334028v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:55,589] [INFO] Task started: Blastn
[2024-01-24 11:35:55,589] [INFO] Running command: blastn -query GCF_013340285.1_ASM1334028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ee9f6ab-47ca-46c9-8232-09abbd413962/dqc_reference/reference_markers_gtdb.fasta -out GCF_013340285.1_ASM1334028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:56,473] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:56,476] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:56,477] [INFO] Target genome list was writen to GCF_013340285.1_ASM1334028v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:56,488] [INFO] Task started: fastANI
[2024-01-24 11:35:56,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg298e6509-f7ea-4809-a576-c051fa50dd66/GCF_013340285.1_ASM1334028v1_genomic.fna.gz --refList GCF_013340285.1_ASM1334028v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013340285.1_ASM1334028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:09,003] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:09,013] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:09,013] [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_013340285.1	s__Halodesulfovibrio subterraneus	100.0	1366	1366	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003252375.1	s__Halodesulfovibrio sp003252375	80.8618	624	1366	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_013340305.1	s__Halodesulfovibrio psychrotolerans	79.6412	628	1366	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	77.4693	198	1366	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_000021385.1	s__Cupidesulfovibrio vulgaris_A	77.4621	274	1366	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	97.08	97.08	0.92	0.92	2	-
GCF_000482745.1	s__Oleidesulfovibrio alaskensis	77.4031	203	1366	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Oleidesulfovibrio	95.0	99.29	99.19	0.96	0.95	4	-
GCF_012843875.1	s__Desulfovibrio sp900556755	77.2391	104	1366	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	98.27	96.78	0.88	0.81	10	-
GCF_000156375.1	s__Desulfovibrio piger	77.2341	116	1366	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_900553145.1	s__Bilophila sp900553145	76.7791	84	1366	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701705.1	s__Bilophila wadsworthia	76.6755	95	1366	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_000519125.1	s__Desulfocurvus vexinensis	76.4929	116	1366	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfocurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709205.1	s__JACCQO01 sp015709205	76.4155	133	1366	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_000420485.1	s__Paucidesulfovibrio longus	76.2791	119	1366	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:09,015] [INFO] GTDB search result was written to GCF_013340285.1_ASM1334028v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:09,015] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:09,019] [INFO] DFAST_QC result json was written to GCF_013340285.1_ASM1334028v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:09,019] [INFO] DFAST_QC completed!
[2024-01-24 11:36:09,019] [INFO] Total running time: 0h1m28s