[2024-01-24 11:20:34,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,029] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fab8b47-11de-4654-aa9f-ffd3ed0ac7b1/dqc_reference
[2024-01-24 11:20:35,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,254] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,255] [INFO] Running command: gunzip -c /var/lib/cwl/stged445006-a7c3-46b8-bb6a-1e8384efd18f/GCF_013019105.1_ASM1301910v1_genomic.fna.gz | prodigal -d GCF_013019105.1_ASM1301910v1_genomic.fna/cds.fna -a GCF_013019105.1_ASM1301910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:48,610] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:48,610] [INFO] Task started: HMMsearch
[2024-01-24 11:20:48,610] [INFO] Running command: hmmsearch --tblout GCF_013019105.1_ASM1301910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fab8b47-11de-4654-aa9f-ffd3ed0ac7b1/dqc_reference/reference_markers.hmm GCF_013019105.1_ASM1301910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:48,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:48,889] [INFO] Found 6/6 markers.
[2024-01-24 11:20:48,928] [INFO] Query marker FASTA was written to GCF_013019105.1_ASM1301910v1_genomic.fna/markers.fasta
[2024-01-24 11:20:48,928] [INFO] Task started: Blastn
[2024-01-24 11:20:48,928] [INFO] Running command: blastn -query GCF_013019105.1_ASM1301910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fab8b47-11de-4654-aa9f-ffd3ed0ac7b1/dqc_reference/reference_markers.fasta -out GCF_013019105.1_ASM1301910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:49,626] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:49,630] [INFO] Selected 13 target genomes.
[2024-01-24 11:20:49,630] [INFO] Target genome list was writen to GCF_013019105.1_ASM1301910v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:49,646] [INFO] Task started: fastANI
[2024-01-24 11:20:49,646] [INFO] Running command: fastANI --query /var/lib/cwl/stged445006-a7c3-46b8-bb6a-1e8384efd18f/GCF_013019105.1_ASM1301910v1_genomic.fna.gz --refList GCF_013019105.1_ASM1301910v1_genomic.fna/target_genomes.txt --output GCF_013019105.1_ASM1301910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:00,342] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:00,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fab8b47-11de-4654-aa9f-ffd3ed0ac7b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:00,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fab8b47-11de-4654-aa9f-ffd3ed0ac7b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:00,357] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:00,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:00,358] [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
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	100.0	1459	1460	95	conclusive
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	82.6075	856	1460	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	78.4406	405	1460	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	78.2137	456	1460	95	below_threshold
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	78.063	443	1460	95	below_threshold
Solidesulfovibrio magneticus	strain=RS-1	GCA_000010665.1	184917	184917	type	True	77.9971	452	1460	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	77.8735	392	1460	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.7264	329	1460	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	77.6042	403	1460	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.5476	164	1460	95	below_threshold
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	77.5022	280	1460	95	below_threshold
Desulfocurvibacter africanus subsp. africanus	strain=DSM 2603	GCA_000422545.1	1511600	873	type	True	77.4124	258	1460	95	below_threshold
Brachybacterium nesterenkovii	strain=CIP104813	GCA_900163655.1	47847	47847	type	True	75.2354	65	1460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:00,359] [INFO] DFAST Taxonomy check result was written to GCF_013019105.1_ASM1301910v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:00,360] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:00,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:00,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fab8b47-11de-4654-aa9f-ffd3ed0ac7b1/dqc_reference/checkm_data
[2024-01-24 11:21:00,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:00,401] [INFO] Task started: CheckM
[2024-01-24 11:21:00,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013019105.1_ASM1301910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013019105.1_ASM1301910v1_genomic.fna/checkm_input GCF_013019105.1_ASM1301910v1_genomic.fna/checkm_result
[2024-01-24 11:21:44,249] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:44,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:44,269] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:44,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:44,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013019105.1_ASM1301910v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:44,270] [INFO] Task started: Blastn
[2024-01-24 11:21:44,270] [INFO] Running command: blastn -query GCF_013019105.1_ASM1301910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fab8b47-11de-4654-aa9f-ffd3ed0ac7b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_013019105.1_ASM1301910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:45,412] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:45,416] [INFO] Selected 14 target genomes.
[2024-01-24 11:21:45,417] [INFO] Target genome list was writen to GCF_013019105.1_ASM1301910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:45,439] [INFO] Task started: fastANI
[2024-01-24 11:21:45,439] [INFO] Running command: fastANI --query /var/lib/cwl/stged445006-a7c3-46b8-bb6a-1e8384efd18f/GCF_013019105.1_ASM1301910v1_genomic.fna.gz --refList GCF_013019105.1_ASM1301910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013019105.1_ASM1301910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:56,829] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:56,841] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:56,841] [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_013019105.1	s__Fundidesulfovibrio sp013019105	100.0	1459	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000429325.1	s__Fundidesulfovibrio putealis	82.616	855	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773665.1	s__Fundidesulfovibrio sp009773665	81.6329	532	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208105.1	s__Fundidesulfovibrio sp016208105	80.5837	666	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	99.98	99.98	0.95	0.95	2	-
GCA_002382645.1	s__Aminidesulfovibrio sp002382645	78.2898	368	1460	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_000702665.1	s__Solidesulfovibrio alcoholivorans	78.2218	455	1460	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_003525525.1	s__Solidesulfovibrio sp003525525	78.1478	289	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376475.1	s__Desulfolutivibrio sulfoxidireducens	77.9491	414	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.21	99.21	0.94	0.94	2	-
GCF_000504305.1	s__Cupidesulfovibrio termitidis	77.7716	327	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	98.21	98.21	0.92	0.92	2	-
GCA_002452635.1	s__UBA6814 sp002452635	77.7299	360	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__UBA6814	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177215.2	s__Solidesulfovibrio carbinoliphilus	77.5854	406	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936595.1	s__Solidesulfovibrio sp001936595	77.3744	351	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801335.2	s__Solidesulfovibrio sp000801335	77.3499	319	1460	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_002369295.1	s__Desulfovibrio sp002369295	76.5336	106	1460	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.45	99.45	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:56,842] [INFO] GTDB search result was written to GCF_013019105.1_ASM1301910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:56,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:56,848] [INFO] DFAST_QC result json was written to GCF_013019105.1_ASM1301910v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:56,848] [INFO] DFAST_QC completed!
[2024-01-24 11:21:56,848] [INFO] Total running time: 0h1m23s