[2024-01-24 14:06:06,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ba5ddb3-c5ad-46da-8fe6-8be69acfffa8/dqc_reference
[2024-01-24 14:06:07,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,418] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,418] [INFO] Running command: gunzip -c /var/lib/cwl/stg51380186-bbd7-4a17-9e00-1768a50b12a8/GCF_003987515.1_ASM398751v1_genomic.fna.gz | prodigal -d GCF_003987515.1_ASM398751v1_genomic.fna/cds.fna -a GCF_003987515.1_ASM398751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:11,693] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:11,693] [INFO] Task started: HMMsearch
[2024-01-24 14:06:11,693] [INFO] Running command: hmmsearch --tblout GCF_003987515.1_ASM398751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ba5ddb3-c5ad-46da-8fe6-8be69acfffa8/dqc_reference/reference_markers.hmm GCF_003987515.1_ASM398751v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:11,943] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:11,944] [INFO] Found 6/6 markers.
[2024-01-24 14:06:11,974] [INFO] Query marker FASTA was written to GCF_003987515.1_ASM398751v1_genomic.fna/markers.fasta
[2024-01-24 14:06:11,975] [INFO] Task started: Blastn
[2024-01-24 14:06:11,975] [INFO] Running command: blastn -query GCF_003987515.1_ASM398751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ba5ddb3-c5ad-46da-8fe6-8be69acfffa8/dqc_reference/reference_markers.fasta -out GCF_003987515.1_ASM398751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:12,589] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:12,592] [INFO] Selected 22 target genomes.
[2024-01-24 14:06:12,593] [INFO] Target genome list was writen to GCF_003987515.1_ASM398751v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:12,634] [INFO] Task started: fastANI
[2024-01-24 14:06:12,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg51380186-bbd7-4a17-9e00-1768a50b12a8/GCF_003987515.1_ASM398751v1_genomic.fna.gz --refList GCF_003987515.1_ASM398751v1_genomic.fna/target_genomes.txt --output GCF_003987515.1_ASM398751v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:24,856] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:24,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ba5ddb3-c5ad-46da-8fe6-8be69acfffa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:24,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ba5ddb3-c5ad-46da-8fe6-8be69acfffa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:24,871] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:24,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:24,872] [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
Vagococcus penaei	strain=LMG 24833	GCA_003987515.1	633807	633807	type	True	100.0	751	751	95	conclusive
Vagococcus penaei	strain=CD276	GCA_001998885.1	633807	633807	type	True	99.9869	739	751	95	conclusive
Vagococcus vulneris	strain=SS1995	GCA_003950515.1	1977869	1977869	type	True	79.1461	242	751	95	below_threshold
Vagococcus silagei	strain=2B-2	GCA_004795745.1	2508885	2508885	type	True	79.017	170	751	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	78.5929	155	751	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	78.5208	185	751	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	78.3298	178	751	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	78.1784	182	751	95	below_threshold
Enterococcus cecorum	strain=ATCC 43198	GCA_000492155.1	44008	44008	type	True	78.0966	70	751	95	below_threshold
Vagococcus humatus	strain=JCM 31581	GCA_003950325.1	1889241	1889241	type	True	78.074	70	751	95	below_threshold
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	77.8004	72	751	95	below_threshold
Enterococcus aquimarinus	strain=DSM 17690	GCA_001885765.1	328396	328396	type	True	77.7626	65	751	95	below_threshold
Enterococcus pseudoavium	strain=NBRC 100491	GCA_001544295.1	44007	44007	type	True	77.6002	52	751	95	below_threshold
Isobaculum melis	strain=DSM 13760	GCA_900111355.1	142588	142588	type	True	77.5295	75	751	95	below_threshold
Carnobacterium inhibens subsp. gilichinskyi	strain=WN1359	GCA_000493735.1	1266845	147709	type	True	77.4903	51	751	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.466	65	751	95	below_threshold
Catellicoccus marimammalium	strain=M35/04/3	GCA_000313915.1	300419	300419	type	True	77.1696	53	751	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:24,874] [INFO] DFAST Taxonomy check result was written to GCF_003987515.1_ASM398751v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:24,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:24,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:24,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ba5ddb3-c5ad-46da-8fe6-8be69acfffa8/dqc_reference/checkm_data
[2024-01-24 14:06:24,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:24,902] [INFO] Task started: CheckM
[2024-01-24 14:06:24,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987515.1_ASM398751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987515.1_ASM398751v1_genomic.fna/checkm_input GCF_003987515.1_ASM398751v1_genomic.fna/checkm_result
[2024-01-24 14:06:46,002] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:46,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:46,025] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:46,026] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:46,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987515.1_ASM398751v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:46,027] [INFO] Task started: Blastn
[2024-01-24 14:06:46,027] [INFO] Running command: blastn -query GCF_003987515.1_ASM398751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ba5ddb3-c5ad-46da-8fe6-8be69acfffa8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987515.1_ASM398751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:46,815] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:46,818] [INFO] Selected 25 target genomes.
[2024-01-24 14:06:46,819] [INFO] Target genome list was writen to GCF_003987515.1_ASM398751v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:46,840] [INFO] Task started: fastANI
[2024-01-24 14:06:46,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg51380186-bbd7-4a17-9e00-1768a50b12a8/GCF_003987515.1_ASM398751v1_genomic.fna.gz --refList GCF_003987515.1_ASM398751v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987515.1_ASM398751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:58,645] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:58,664] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:58,665] [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_001998885.1	s__Vagococcus penaei	99.9869	739	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_003950515.1	s__Vagococcus vulneris	79.1461	242	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795745.1	s__Vagococcus silagei	78.9878	172	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003950315.1	s__Vagococcus bubulae	78.5929	155	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397115.1	s__Vagococcus carniphilus	78.5208	185	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001870205.1	s__Vagococcus teuberi	78.469	148	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	98.63	98.63	0.90	0.90	3	-
GCF_011304195.1	s__Vagococcus hydrophili	78.3035	178	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017316185.1	s__Vagococcus sp017316185	78.2156	162	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337315.1	s__Vagococcus fluvialis	78.1987	181	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_003950325.1	s__Vagococcus_C humatus	78.0268	69	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163795.1	s__Vagococcus fluvialis_A	77.991	192	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000407285.1	s__Enterococcus_F saccharolyticus	77.8189	77	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001465345.1	s__Enterococcus rotai	77.8004	72	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885765.1	s__Enterococcus_I aquimarinus	77.7626	65	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	98.10	98.04	0.96	0.95	6	-
GCF_001544295.1	s__Enterococcus_A pseudoavium	77.6002	52	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017316125.1	s__Enterococcus_B sp017316125	77.4497	77	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730285.1	s__Enterococcus ureasiticus	77.415	87	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.2554	89	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120335.1	s__Enterococcus_E stercoripullorum	77.2489	62	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313915.1	s__Catellicoccus marimammalium	77.1696	53	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Catellicoccaceae;g__Catellicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000270185.1	s__Melissococcus plutonius	77.1635	63	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Melissococcus	95.0	99.79	99.26	0.98	0.96	19	-
GCF_017315945.1	s__Enterococcus_B sp017315945	77.0781	87	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116505.1	s__Enterococcus_I avicola	77.0119	66	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:58,666] [INFO] GTDB search result was written to GCF_003987515.1_ASM398751v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:58,667] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:58,672] [INFO] DFAST_QC result json was written to GCF_003987515.1_ASM398751v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:58,672] [INFO] DFAST_QC completed!
[2024-01-24 14:06:58,672] [INFO] Total running time: 0h0m53s