[2024-01-25 18:15:20,921] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:20,923] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:20,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cfb9653-884c-4716-b6b8-473c2f6df1c8/dqc_reference
[2024-01-25 18:15:22,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:22,060] [INFO] Task started: Prodigal
[2024-01-25 18:15:22,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f377f41-0538-495b-a69b-d2b60b064546/GCF_024637875.1_ASM2463787v1_genomic.fna.gz | prodigal -d GCF_024637875.1_ASM2463787v1_genomic.fna/cds.fna -a GCF_024637875.1_ASM2463787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:25,637] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:25,637] [INFO] Task started: HMMsearch
[2024-01-25 18:15:25,637] [INFO] Running command: hmmsearch --tblout GCF_024637875.1_ASM2463787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cfb9653-884c-4716-b6b8-473c2f6df1c8/dqc_reference/reference_markers.hmm GCF_024637875.1_ASM2463787v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:25,847] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:25,849] [INFO] Found 6/6 markers.
[2024-01-25 18:15:25,871] [INFO] Query marker FASTA was written to GCF_024637875.1_ASM2463787v1_genomic.fna/markers.fasta
[2024-01-25 18:15:25,871] [INFO] Task started: Blastn
[2024-01-25 18:15:25,871] [INFO] Running command: blastn -query GCF_024637875.1_ASM2463787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cfb9653-884c-4716-b6b8-473c2f6df1c8/dqc_reference/reference_markers.fasta -out GCF_024637875.1_ASM2463787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:26,444] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:26,447] [INFO] Selected 18 target genomes.
[2024-01-25 18:15:26,447] [INFO] Target genome list was writen to GCF_024637875.1_ASM2463787v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:26,463] [INFO] Task started: fastANI
[2024-01-25 18:15:26,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f377f41-0538-495b-a69b-d2b60b064546/GCF_024637875.1_ASM2463787v1_genomic.fna.gz --refList GCF_024637875.1_ASM2463787v1_genomic.fna/target_genomes.txt --output GCF_024637875.1_ASM2463787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:35,015] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:35,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cfb9653-884c-4716-b6b8-473c2f6df1c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:35,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cfb9653-884c-4716-b6b8-473c2f6df1c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:35,027] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:15:35,028] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:15:35,028] [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 bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	90.75	592	716	95	below_threshold
Vagococcus martis	strain=D7T301	GCA_002026305.1	1768210	1768210	type	True	86.3227	539	716	95	below_threshold
Vagococcus teuberi	strain=DSM 21459	GCA_001870205.1	519472	519472	type	True	86.0951	519	716	95	below_threshold
Granulicatella adiacens	strain=ATCC 49175	GCA_025150565.1	46124	46124	type	True	79.9461	52	716	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	79.228	198	716	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	78.6817	88	716	95	below_threshold
Vagococcus fluvialis	strain=NCDO 2497	GCA_003987575.1	2738	2738	type	True	78.5522	221	716	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	78.5048	107	716	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	78.4908	245	716	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	78.4725	216	716	95	below_threshold
Vagococcus vulneris	strain=SS1995	GCA_003950515.1	1977869	1977869	type	True	78.082	127	716	95	below_threshold
Enterococcus saccharolyticus	strain=DSM 20726	GCA_001886235.1	41997	41997	type	True	77.6793	85	716	95	below_threshold
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	77.5488	84	716	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	77.3786	66	716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:35,029] [INFO] DFAST Taxonomy check result was written to GCF_024637875.1_ASM2463787v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:35,029] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:35,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:35,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cfb9653-884c-4716-b6b8-473c2f6df1c8/dqc_reference/checkm_data
[2024-01-25 18:15:35,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:35,075] [INFO] Task started: CheckM
[2024-01-25 18:15:35,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024637875.1_ASM2463787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024637875.1_ASM2463787v1_genomic.fna/checkm_input GCF_024637875.1_ASM2463787v1_genomic.fna/checkm_result
[2024-01-25 18:15:52,423] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:52,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:52,441] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:52,442] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:52,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024637875.1_ASM2463787v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:52,442] [INFO] Task started: Blastn
[2024-01-25 18:15:52,442] [INFO] Running command: blastn -query GCF_024637875.1_ASM2463787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cfb9653-884c-4716-b6b8-473c2f6df1c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_024637875.1_ASM2463787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:53,223] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:53,226] [INFO] Selected 9 target genomes.
[2024-01-25 18:15:53,226] [INFO] Target genome list was writen to GCF_024637875.1_ASM2463787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:53,232] [INFO] Task started: fastANI
[2024-01-25 18:15:53,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f377f41-0538-495b-a69b-d2b60b064546/GCF_024637875.1_ASM2463787v1_genomic.fna.gz --refList GCF_024637875.1_ASM2463787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024637875.1_ASM2463787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:58,358] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:58,364] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:15:58,365] [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_003462485.1	s__Vagococcus sp003462485	93.996	598	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003950315.1	s__Vagococcus bubulae	90.727	593	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002026305.1	s__Vagococcus martis	86.2866	541	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	N/A	N/A	N/A	N/A	1	-
GCF_001870205.1	s__Vagococcus teuberi	86.0951	519	716	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	79.1386	197	716	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	78.9009	184	716	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	78.512	246	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337315.1	s__Vagococcus fluvialis	78.5069	215	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_900163795.1	s__Vagococcus fluvialis_A	78.4261	182	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:58,366] [INFO] GTDB search result was written to GCF_024637875.1_ASM2463787v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:58,367] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:58,369] [INFO] DFAST_QC result json was written to GCF_024637875.1_ASM2463787v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:58,369] [INFO] DFAST_QC completed!
[2024-01-25 18:15:58,369] [INFO] Total running time: 0h0m37s