[2024-01-24 10:47:40,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg5446d101-1189-498e-82fc-774024edf756/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stga9f09d53-8435-41a4-951c-31c2873fcdb9/GCF_004795745.1_ASM479574v1_genomic.fna.gz | prodigal -d GCF_004795745.1_ASM479574v1_genomic.fna/cds.fna -a GCF_004795745.1_ASM479574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:49,577] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:49,577] [INFO] Task started: HMMsearch
[2024-01-24 10:47:49,577] [INFO] Running command: hmmsearch --tblout GCF_004795745.1_ASM479574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5446d101-1189-498e-82fc-774024edf756/dqc_reference/reference_markers.hmm GCF_004795745.1_ASM479574v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:49,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:49,829] [INFO] Found 6/6 markers.
[2024-01-24 10:47:49,853] [INFO] Query marker FASTA was written to GCF_004795745.1_ASM479574v1_genomic.fna/markers.fasta
[2024-01-24 10:47:49,853] [INFO] Task started: Blastn
[2024-01-24 10:47:49,853] [INFO] Running command: blastn -query GCF_004795745.1_ASM479574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5446d101-1189-498e-82fc-774024edf756/dqc_reference/reference_markers.fasta -out GCF_004795745.1_ASM479574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:50,831] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:50,837] [INFO] Selected 20 target genomes.
[2024-01-24 10:47:50,837] [INFO] Target genome list was writen to GCF_004795745.1_ASM479574v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:50,871] [INFO] Task started: fastANI
[2024-01-24 10:47:50,872] [INFO] Running command: fastANI --query /var/lib/cwl/stga9f09d53-8435-41a4-951c-31c2873fcdb9/GCF_004795745.1_ASM479574v1_genomic.fna.gz --refList GCF_004795745.1_ASM479574v1_genomic.fna/target_genomes.txt --output GCF_004795745.1_ASM479574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:59,716] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:59,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5446d101-1189-498e-82fc-774024edf756/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:59,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5446d101-1189-498e-82fc-774024edf756/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:59,736] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:59,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:59,737] [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 silagei	strain=2B-2	GCA_004795745.1	2508885	2508885	type	True	100.0	812	818	95	conclusive
Vagococcus penaei	strain=CD276	GCA_001998885.1	633807	633807	type	True	79.0693	177	818	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	79.0555	197	818	95	below_threshold
Vagococcus penaei	strain=LMG 24833	GCA_003987515.1	633807	633807	type	True	78.9315	180	818	95	below_threshold
Vagococcus martis	strain=D7T301	GCA_002026305.1	1768210	1768210	type	True	78.609	137	818	95	below_threshold
Vagococcus vulneris	strain=SS1995	GCA_003950515.1	1977869	1977869	type	True	78.2939	148	818	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	78.2007	201	818	95	below_threshold
Vagococcus fluvialis	strain=NCDO 2497	GCA_003987575.1	2738	2738	type	True	78.1458	204	818	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	78.0883	95	818	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	78.0315	151	818	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	77.9305	55	818	95	below_threshold
Vagococcus fessus	strain=CCUG 41755	GCA_003987565.1	120370	120370	type	True	77.7587	93	818	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	77.5957	83	818	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000394015.1	155617	155617	type	True	77.4698	84	818	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407285.1	1814218	41997	type	True	77.4274	85	818	95	below_threshold
Enterococcus saccharolyticus	strain=DSM 20726	GCA_001886235.1	41997	41997	type	True	77.4263	82	818	95	below_threshold
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	77.3865	83	818	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.0755	81	818	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:59,739] [INFO] DFAST Taxonomy check result was written to GCF_004795745.1_ASM479574v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:59,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:59,740] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:59,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5446d101-1189-498e-82fc-774024edf756/dqc_reference/checkm_data
[2024-01-24 10:47:59,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:59,784] [INFO] Task started: CheckM
[2024-01-24 10:47:59,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004795745.1_ASM479574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004795745.1_ASM479574v1_genomic.fna/checkm_input GCF_004795745.1_ASM479574v1_genomic.fna/checkm_result
[2024-01-24 10:48:21,504] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:21,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:21,521] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:21,522] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:21,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004795745.1_ASM479574v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:21,523] [INFO] Task started: Blastn
[2024-01-24 10:48:21,523] [INFO] Running command: blastn -query GCF_004795745.1_ASM479574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5446d101-1189-498e-82fc-774024edf756/dqc_reference/reference_markers_gtdb.fasta -out GCF_004795745.1_ASM479574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:22,419] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:22,423] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:22,423] [INFO] Target genome list was writen to GCF_004795745.1_ASM479574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:22,437] [INFO] Task started: fastANI
[2024-01-24 10:48:22,438] [INFO] Running command: fastANI --query /var/lib/cwl/stga9f09d53-8435-41a4-951c-31c2873fcdb9/GCF_004795745.1_ASM479574v1_genomic.fna.gz --refList GCF_004795745.1_ASM479574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004795745.1_ASM479574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:29,893] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:29,908] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:29,908] [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_004795745.1	s__Vagococcus silagei	100.0	812	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001998885.1	s__Vagococcus penaei	79.0872	177	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_014397115.1	s__Vagococcus carniphilus	79.0777	197	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002026305.1	s__Vagococcus martis	78.5821	138	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	N/A	N/A	N/A	N/A	1	-
GCF_011304195.1	s__Vagococcus hydrophili	78.492	178	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163795.1	s__Vagococcus fluvialis_A	78.3355	182	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003950515.1	s__Vagococcus vulneris	78.2939	148	818	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	78.2277	199	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_004792515.1	s__Vagococcus_A sp004792515	78.0883	95	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003950315.1	s__Vagococcus bubulae	78.0556	150	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000271405.2	s__Enterococcus_B hirae	77.9906	57	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.97	97.87	0.92	0.86	203	-
GCF_003987565.1	s__Vagococcus_D fessus	77.7587	93	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001465345.1	s__Enterococcus rotai	77.6351	69	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407445.1	s__Enterococcus moraviensis	77.5617	85	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000407285.1	s__Enterococcus_F saccharolyticus	77.4595	84	818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:29,909] [INFO] GTDB search result was written to GCF_004795745.1_ASM479574v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:29,910] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:29,916] [INFO] DFAST_QC result json was written to GCF_004795745.1_ASM479574v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:29,916] [INFO] DFAST_QC completed!
[2024-01-24 10:48:29,916] [INFO] Total running time: 0h0m49s