[2024-01-24 11:05:49,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a00425d-c305-4682-bba4-ea2dbee8bf2f/dqc_reference
[2024-01-24 11:05:51,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,279] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,280] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9ebc16d-768b-4295-b028-63dc50b19eb4/GCF_000744945.1_ASM74494v1_genomic.fna.gz | prodigal -d GCF_000744945.1_ASM74494v1_genomic.fna/cds.fna -a GCF_000744945.1_ASM74494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:58,203] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:58,203] [INFO] Task started: HMMsearch
[2024-01-24 11:05:58,203] [INFO] Running command: hmmsearch --tblout GCF_000744945.1_ASM74494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a00425d-c305-4682-bba4-ea2dbee8bf2f/dqc_reference/reference_markers.hmm GCF_000744945.1_ASM74494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:58,412] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:58,413] [INFO] Found 6/6 markers.
[2024-01-24 11:05:58,440] [INFO] Query marker FASTA was written to GCF_000744945.1_ASM74494v1_genomic.fna/markers.fasta
[2024-01-24 11:05:58,441] [INFO] Task started: Blastn
[2024-01-24 11:05:58,441] [INFO] Running command: blastn -query GCF_000744945.1_ASM74494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a00425d-c305-4682-bba4-ea2dbee8bf2f/dqc_reference/reference_markers.fasta -out GCF_000744945.1_ASM74494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:59,300] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:59,303] [INFO] Selected 23 target genomes.
[2024-01-24 11:05:59,303] [INFO] Target genome list was writen to GCF_000744945.1_ASM74494v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:59,326] [INFO] Task started: fastANI
[2024-01-24 11:05:59,326] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ebc16d-768b-4295-b028-63dc50b19eb4/GCF_000744945.1_ASM74494v1_genomic.fna.gz --refList GCF_000744945.1_ASM74494v1_genomic.fna/target_genomes.txt --output GCF_000744945.1_ASM74494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:12,049] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:12,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a00425d-c305-4682-bba4-ea2dbee8bf2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:12,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a00425d-c305-4682-bba4-ea2dbee8bf2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:12,064] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:12,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:12,064] [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
Carnobacterium maltaromaticum	strain=MX5	GCA_000744945.1	2751	2751	type	True	100.0	1284	1290	95	conclusive
Carnobacterium maltaromaticum	strain=DSM 20342	GCA_001437315.1	2751	2751	type	True	99.9448	1202	1290	95	conclusive
Jeotgalibaca arthritidis	strain=CECT 9157	GCA_011100465.1	1868794	1868794	type	True	81.0458	54	1290	95	below_threshold
Carnobacterium gallinarum	strain=MT44	GCA_000744375.1	2749	2749	type	True	81.0239	542	1290	95	below_threshold
Carnobacterium divergens	strain=NCTC13772	GCA_900446755.1	2748	2748	type	True	79.4911	327	1290	95	below_threshold
Carnobacterium divergens	strain=66	GCA_000744255.1	2748	2748	type	True	79.4289	323	1290	95	below_threshold
Carnobacterium inhibens subsp. gilichinskyi	strain=WN1359	GCA_000493735.1	1266845	147709	type	True	79.3284	137	1290	95	below_threshold
Carnobacterium divergens	strain=DSM 20623	GCA_001437085.1	2748	2748	type	True	78.9468	319	1290	95	below_threshold
Carnobacterium inhibens subsp. inhibens	strain=K1	GCA_000746825.1	1758721	147709	type	True	78.9358	127	1290	95	below_threshold
Enterococcus gallinarum	strain=NCTC12359	GCA_900447935.1	1353	1353	suspected-type	True	78.8774	64	1290	95	below_threshold
Vagococcus coleopterorum	strain=HDW17A	GCA_011303955.1	2714946	2714946	type	True	78.8195	74	1290	95	below_threshold
Carnobacterium mobile	strain=MT37L	GCA_000744825.1	2750	2750	type	True	78.7484	129	1290	95	below_threshold
Carnobacterium viridans	strain=MPL-11	GCA_900102725.1	174587	174587	type	True	78.7392	151	1290	95	below_threshold
Carnobacterium funditum	strain=pf3	GCA_000744185.1	2752	2752	type	True	78.6549	134	1290	95	below_threshold
Carnobacterium jeotgali	strain=MS3	GCA_000708655.1	545534	545534	type	True	78.5262	122	1290	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	77.9074	53	1290	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	77.8593	116	1290	95	below_threshold
Enterococcus gallinarum	strain=DSM 24841	GCA_001886155.1	1353	1353	suspected-type	True	76.4479	53	1290	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:12,066] [INFO] DFAST Taxonomy check result was written to GCF_000744945.1_ASM74494v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:12,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:12,067] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:12,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a00425d-c305-4682-bba4-ea2dbee8bf2f/dqc_reference/checkm_data
[2024-01-24 11:06:12,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:12,133] [INFO] Task started: CheckM
[2024-01-24 11:06:12,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000744945.1_ASM74494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000744945.1_ASM74494v1_genomic.fna/checkm_input GCF_000744945.1_ASM74494v1_genomic.fna/checkm_result
[2024-01-24 11:06:37,643] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:37,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 11:06:37,664] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:37,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:37,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000744945.1_ASM74494v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:37,664] [INFO] Task started: Blastn
[2024-01-24 11:06:37,665] [INFO] Running command: blastn -query GCF_000744945.1_ASM74494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a00425d-c305-4682-bba4-ea2dbee8bf2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000744945.1_ASM74494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:38,423] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:38,426] [INFO] Selected 21 target genomes.
[2024-01-24 11:06:38,427] [INFO] Target genome list was writen to GCF_000744945.1_ASM74494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:38,439] [INFO] Task started: fastANI
[2024-01-24 11:06:38,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ebc16d-768b-4295-b028-63dc50b19eb4/GCF_000744945.1_ASM74494v1_genomic.fna.gz --refList GCF_000744945.1_ASM74494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000744945.1_ASM74494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:51,174] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:51,188] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:51,188] [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_000744945.1	s__Carnobacterium maltaromaticum	100.0	1285	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	98.15	96.42	0.90	0.81	35	conclusive
GCF_000744375.1	s__Carnobacterium gallinarum	81.0393	543	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011100465.1	s__Jeotgalibaca arthritidis	80.9964	55	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Jeotgalibaca	95.0	97.70	97.22	0.78	0.71	3	-
GCF_000745125.1	s__Carnobacterium_A jeotgali	80.1148	142	1290	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_000744255.1	s__Carnobacterium divergens	79.4547	322	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.06	98.93	0.92	0.90	24	-
GCF_003795125.1	s__Tetragenococcus osmophilus	79.2441	62	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258435.1	s__Carnobacterium divergens_A	79.1703	333	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.21	98.87	0.95	0.92	17	-
GCF_000746825.1	s__Carnobacterium_A inhibens	79.0155	128	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
GCF_000744825.1	s__Carnobacterium_A mobile	78.8569	130	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	97.99	97.99	0.87	0.87	2	-
GCF_900102725.1	s__Carnobacterium_A viridans	78.7596	151	1290	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_000195575.1	s__Carnobacterium_A sp000195575	78.749	137	1290	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_000744185.1	s__Carnobacterium_A funditum	78.6104	135	1290	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_900177385.1	s__Carnobacterium_A iners	78.3952	142	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001730285.1	s__Enterococcus ureasiticus	77.3315	101	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCF_003337315.1	s__Vagococcus fluvialis	77.1199	96	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_009933335.1	s__Enterococcus_F sp009933335	77.0768	87	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377505.1	s__Enterococcus sp017377505	77.0117	111	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_001544275.1	s__Enterococcus_D gallinarum	76.8057	56	1290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.60	97.23	0.85	0.80	74	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:51,190] [INFO] GTDB search result was written to GCF_000744945.1_ASM74494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:51,190] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:51,194] [INFO] DFAST_QC result json was written to GCF_000744945.1_ASM74494v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:51,194] [INFO] DFAST_QC completed!
[2024-01-24 11:06:51,194] [INFO] Total running time: 0h1m2s