[2024-01-24 14:19:15,660] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,662] [INFO] DQC Reference Directory: /var/lib/cwl/stgf00c1e70-0f8d-4cdd-9ca7-721ab62637a2/dqc_reference
[2024-01-24 14:19:18,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,320] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,320] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9429e98-5ab9-499c-92c1-db17b462889f/GCF_001046995.1_ASM104699v1_genomic.fna.gz | prodigal -d GCF_001046995.1_ASM104699v1_genomic.fna/cds.fna -a GCF_001046995.1_ASM104699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:23,428] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:23,428] [INFO] Task started: HMMsearch
[2024-01-24 14:19:23,428] [INFO] Running command: hmmsearch --tblout GCF_001046995.1_ASM104699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf00c1e70-0f8d-4cdd-9ca7-721ab62637a2/dqc_reference/reference_markers.hmm GCF_001046995.1_ASM104699v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:23,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:23,961] [INFO] Found 6/6 markers.
[2024-01-24 14:19:23,990] [INFO] Query marker FASTA was written to GCF_001046995.1_ASM104699v1_genomic.fna/markers.fasta
[2024-01-24 14:19:23,990] [INFO] Task started: Blastn
[2024-01-24 14:19:23,990] [INFO] Running command: blastn -query GCF_001046995.1_ASM104699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf00c1e70-0f8d-4cdd-9ca7-721ab62637a2/dqc_reference/reference_markers.fasta -out GCF_001046995.1_ASM104699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:27,276] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:27,279] [INFO] Selected 12 target genomes.
[2024-01-24 14:19:27,279] [INFO] Target genome list was writen to GCF_001046995.1_ASM104699v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:27,287] [INFO] Task started: fastANI
[2024-01-24 14:19:27,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9429e98-5ab9-499c-92c1-db17b462889f/GCF_001046995.1_ASM104699v1_genomic.fna.gz --refList GCF_001046995.1_ASM104699v1_genomic.fna/target_genomes.txt --output GCF_001046995.1_ASM104699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:36,241] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:36,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf00c1e70-0f8d-4cdd-9ca7-721ab62637a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:36,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf00c1e70-0f8d-4cdd-9ca7-721ab62637a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:36,301] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:19:36,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:36,301] [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
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	100.0	910	912	95	conclusive
Mammaliicoccus sciuri	strain=NCTC12103	GCA_900474615.1	1296	1296	type	True	99.9975	912	912	95	conclusive
Mammaliicoccus sciuri	strain=NCTC 12103	GCA_002901825.1	1296	1296	type	True	99.9838	904	912	95	conclusive
Mammaliicoccus vitulinus	strain=DSM 15615	GCA_002902265.1	71237	71237	type	True	84.4032	615	912	95	below_threshold
Mammaliicoccus fleurettii	strain=DSM 13212	GCA_003970575.1	150056	150056	type	True	84.3557	614	912	95	below_threshold
Mammaliicoccus vitulinus	strain=FDAARGOS_1207	GCA_016889245.1	71237	71237	suspected-type	True	84.3309	682	912	95	below_threshold
Mammaliicoccus fleurettii	strain=NCTC13829	GCA_900458505.1	150056	150056	type	True	84.1953	659	912	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	78.2434	119	912	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	76.2872	52	912	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	75.7874	52	912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:36,305] [INFO] DFAST Taxonomy check result was written to GCF_001046995.1_ASM104699v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:36,306] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:36,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:36,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf00c1e70-0f8d-4cdd-9ca7-721ab62637a2/dqc_reference/checkm_data
[2024-01-24 14:19:36,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:36,345] [INFO] Task started: CheckM
[2024-01-24 14:19:36,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001046995.1_ASM104699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001046995.1_ASM104699v1_genomic.fna/checkm_input GCF_001046995.1_ASM104699v1_genomic.fna/checkm_result
[2024-01-24 14:20:05,141] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:05,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:05,164] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:05,164] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:05,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001046995.1_ASM104699v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:05,165] [INFO] Task started: Blastn
[2024-01-24 14:20:05,165] [INFO] Running command: blastn -query GCF_001046995.1_ASM104699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf00c1e70-0f8d-4cdd-9ca7-721ab62637a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001046995.1_ASM104699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:07,714] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:07,718] [INFO] Selected 8 target genomes.
[2024-01-24 14:20:07,719] [INFO] Target genome list was writen to GCF_001046995.1_ASM104699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:07,723] [INFO] Task started: fastANI
[2024-01-24 14:20:07,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9429e98-5ab9-499c-92c1-db17b462889f/GCF_001046995.1_ASM104699v1_genomic.fna.gz --refList GCF_001046995.1_ASM104699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001046995.1_ASM104699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:12,988] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:13,004] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:13,005] [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_002901825.1	s__Mammaliicoccus sciuri	99.9838	904	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	conclusive
GCF_002902265.1	s__Mammaliicoccus vitulinus	84.3927	616	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	98.82	98.52	0.92	0.85	19	-
GCF_003970575.1	s__Mammaliicoccus fleurettii	84.3703	613	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.35	98.97	0.91	0.88	9	-
GCF_002902755.1	s__Mammaliicoccus lentus	81.8742	555	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.03	97.66	0.94	0.90	21	-
GCF_002902525.1	s__Mammaliicoccus stepanovicii	81.1787	508	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	100.00	100.00	1.00	0.99	3	-
GCF_004117835.1	s__Macrococcus_B sp004117835	77.9638	177	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010125.1	s__Staphylococcus saprophyticus	77.2833	171	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:13,006] [INFO] GTDB search result was written to GCF_001046995.1_ASM104699v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:13,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:13,010] [INFO] DFAST_QC result json was written to GCF_001046995.1_ASM104699v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:13,010] [INFO] DFAST_QC completed!
[2024-01-24 14:20:13,011] [INFO] Total running time: 0h0m57s