[2024-01-24 11:48:21,285] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg695f61ca-9c8a-418d-8547-3a48000f807a/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stga8da3281-1c8b-4e14-96dd-ed0f48937e16/GCF_020735385.1_ASM2073538v1_genomic.fna.gz | prodigal -d GCF_020735385.1_ASM2073538v1_genomic.fna/cds.fna -a GCF_020735385.1_ASM2073538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:28,184] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:28,184] [INFO] Task started: HMMsearch
[2024-01-24 11:48:28,184] [INFO] Running command: hmmsearch --tblout GCF_020735385.1_ASM2073538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg695f61ca-9c8a-418d-8547-3a48000f807a/dqc_reference/reference_markers.hmm GCF_020735385.1_ASM2073538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:28,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:28,429] [INFO] Found 6/6 markers.
[2024-01-24 11:48:28,446] [INFO] Query marker FASTA was written to GCF_020735385.1_ASM2073538v1_genomic.fna/markers.fasta
[2024-01-24 11:48:28,446] [INFO] Task started: Blastn
[2024-01-24 11:48:28,447] [INFO] Running command: blastn -query GCF_020735385.1_ASM2073538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg695f61ca-9c8a-418d-8547-3a48000f807a/dqc_reference/reference_markers.fasta -out GCF_020735385.1_ASM2073538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:30,205] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:30,210] [INFO] Selected 25 target genomes.
[2024-01-24 11:48:30,210] [INFO] Target genome list was writen to GCF_020735385.1_ASM2073538v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:30,427] [INFO] Task started: fastANI
[2024-01-24 11:48:30,427] [INFO] Running command: fastANI --query /var/lib/cwl/stga8da3281-1c8b-4e14-96dd-ed0f48937e16/GCF_020735385.1_ASM2073538v1_genomic.fna.gz --refList GCF_020735385.1_ASM2073538v1_genomic.fna/target_genomes.txt --output GCF_020735385.1_ASM2073538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:39,788] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:39,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg695f61ca-9c8a-418d-8547-3a48000f807a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:39,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg695f61ca-9c8a-418d-8547-3a48000f807a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:39,801] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:48:39,802] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:48:39,802] [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
Granulicatella adiacens	strain=FDAARGOS_1477	GCA_019931005.1	46124	46124	type	True	80.4065	207	630	95	below_threshold
Granulicatella adiacens	strain=ATCC 49175	GCA_025150565.1	46124	46124	type	True	80.311	208	630	95	below_threshold
Granulicatella adiacens	strain=ATCC 49175	GCA_000160675.1	46124	46124	type	True	79.8219	202	630	95	below_threshold
Vagococcus humatus	strain=JCM 31581	GCA_003950325.1	1889241	1889241	type	True	79.6316	54	630	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	79.2535	69	630	95	below_threshold
Granulicatella balaenopterae	strain=DSM 15827	GCA_900111135.1	137733	137733	type	True	78.8963	138	630	95	below_threshold
Carnobacterium viridans	strain=MPL-11	GCA_900102725.1	174587	174587	type	True	78.8476	53	630	95	below_threshold
Carnobacterium gallinarum	strain=MT44	GCA_000744375.1	2749	2749	type	True	78.3532	68	630	95	below_threshold
Carnobacterium jeotgali	strain=MS3	GCA_000745125.1	545534	545534	type	True	78.2356	60	630	95	below_threshold
Vagococcus penaei	strain=CD276	GCA_001998885.1	633807	633807	type	True	78.0091	50	630	95	below_threshold
Carnobacterium jeotgali	strain=MS3	GCA_000708655.1	545534	545534	type	True	77.2556	53	630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:39,804] [INFO] DFAST Taxonomy check result was written to GCF_020735385.1_ASM2073538v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:39,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:39,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:39,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg695f61ca-9c8a-418d-8547-3a48000f807a/dqc_reference/checkm_data
[2024-01-24 11:48:39,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:39,833] [INFO] Task started: CheckM
[2024-01-24 11:48:39,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020735385.1_ASM2073538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020735385.1_ASM2073538v1_genomic.fna/checkm_input GCF_020735385.1_ASM2073538v1_genomic.fna/checkm_result
[2024-01-24 11:48:58,042] [INFO] Task succeeded: CheckM
[2024-01-24 11:48:58,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:48:58,060] [INFO] ===== Completeness check finished =====
[2024-01-24 11:48:58,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:48:58,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020735385.1_ASM2073538v1_genomic.fna/markers.fasta)
[2024-01-24 11:48:58,061] [INFO] Task started: Blastn
[2024-01-24 11:48:58,061] [INFO] Running command: blastn -query GCF_020735385.1_ASM2073538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg695f61ca-9c8a-418d-8547-3a48000f807a/dqc_reference/reference_markers_gtdb.fasta -out GCF_020735385.1_ASM2073538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:58,822] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:58,832] [INFO] Selected 18 target genomes.
[2024-01-24 11:48:58,832] [INFO] Target genome list was writen to GCF_020735385.1_ASM2073538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:48:58,855] [INFO] Task started: fastANI
[2024-01-24 11:48:58,855] [INFO] Running command: fastANI --query /var/lib/cwl/stga8da3281-1c8b-4e14-96dd-ed0f48937e16/GCF_020735385.1_ASM2073538v1_genomic.fna.gz --refList GCF_020735385.1_ASM2073538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020735385.1_ASM2073538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:05,464] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:05,477] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:49:05,477] [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_000162475.2	s__Granulicatella elegans	91.6438	432	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001071995.1	s__Granulicatella sp001071995	80.104	182	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000160675.1	s__Granulicatella adiacens	79.8219	202	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	96.49	96.38	0.91	0.88	11	-
GCA_018364485.1	s__Granulicatella adiacens_A	79.8209	174	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905371865.1	s__Granulicatella sp905371865	79.5317	125	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551535.1	s__Granulicatella sp900551535	79.5283	141	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013874835.1	s__WM01 sp013874835	79.1916	81	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__WM01	95.0	99.19	98.77	0.92	0.86	4	-
GCA_015264885.1	s__Granulicatella sp015264885	78.9892	131	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	95.15	95.15	0.88	0.88	2	-
GCF_900111135.1	s__Granulicatella balaenopterae	78.8963	138	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102725.1	s__Carnobacterium_A viridans	78.8192	52	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.44	98.44	0.88	0.88	2	-
GCF_000745125.1	s__Carnobacterium_A jeotgali	78.73	63	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.33	98.67	0.94	0.87	3	-
GCF_000744375.1	s__Carnobacterium gallinarum	78.5707	69	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570605.1	s__WM01 sp004570605	78.3396	63	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__WM01	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000195575.1	s__Carnobacterium_A sp000195575	77.83	55	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003462485.1	s__Vagococcus sp003462485	77.759	59	630	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:49:05,479] [INFO] GTDB search result was written to GCF_020735385.1_ASM2073538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:05,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:05,482] [INFO] DFAST_QC result json was written to GCF_020735385.1_ASM2073538v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:05,482] [INFO] DFAST_QC completed!
[2024-01-24 11:49:05,482] [INFO] Total running time: 0h0m44s