[2024-01-24 12:31:33,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,130] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb79170e-32d2-4245-8590-c0a6659d55fd/dqc_reference
[2024-01-24 12:31:34,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:34,377] [INFO] Task started: Prodigal
[2024-01-24 12:31:34,378] [INFO] Running command: gunzip -c /var/lib/cwl/stga6c388db-9776-4923-a9d9-e2a4508ef2f3/GCF_002902525.1_ASM290252v1_genomic.fna.gz | prodigal -d GCF_002902525.1_ASM290252v1_genomic.fna/cds.fna -a GCF_002902525.1_ASM290252v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:38,346] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:38,346] [INFO] Task started: HMMsearch
[2024-01-24 12:31:38,346] [INFO] Running command: hmmsearch --tblout GCF_002902525.1_ASM290252v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb79170e-32d2-4245-8590-c0a6659d55fd/dqc_reference/reference_markers.hmm GCF_002902525.1_ASM290252v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:38,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:38,540] [INFO] Found 6/6 markers.
[2024-01-24 12:31:38,562] [INFO] Query marker FASTA was written to GCF_002902525.1_ASM290252v1_genomic.fna/markers.fasta
[2024-01-24 12:31:38,563] [INFO] Task started: Blastn
[2024-01-24 12:31:38,563] [INFO] Running command: blastn -query GCF_002902525.1_ASM290252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb79170e-32d2-4245-8590-c0a6659d55fd/dqc_reference/reference_markers.fasta -out GCF_002902525.1_ASM290252v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:39,137] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:39,140] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:39,141] [INFO] Target genome list was writen to GCF_002902525.1_ASM290252v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:39,144] [INFO] Task started: fastANI
[2024-01-24 12:31:39,145] [INFO] Running command: fastANI --query /var/lib/cwl/stga6c388db-9776-4923-a9d9-e2a4508ef2f3/GCF_002902525.1_ASM290252v1_genomic.fna.gz --refList GCF_002902525.1_ASM290252v1_genomic.fna/target_genomes.txt --output GCF_002902525.1_ASM290252v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:46,744] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:46,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb79170e-32d2-4245-8590-c0a6659d55fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:46,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb79170e-32d2-4245-8590-c0a6659d55fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:46,756] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:31:46,756] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:46,756] [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 stepanovicii	strain=DSM 26319	GCA_002902525.1	643214	643214	type	True	100.0	748	750	95	conclusive
Mammaliicoccus stepanovicii	strain=NCTC13839	GCA_900187075.1	643214	643214	type	True	99.9963	749	750	95	conclusive
Mammaliicoccus stepanovicii	strain=CCM 7717	GCA_014635785.1	643214	643214	type	True	99.995	745	750	95	conclusive
Mammaliicoccus fleurettii	strain=DSM 13212	GCA_003970575.1	150056	150056	type	True	81.6034	478	750	95	below_threshold
Mammaliicoccus fleurettii	strain=NCTC13829	GCA_900458505.1	150056	150056	type	True	81.5674	505	750	95	below_threshold
Mammaliicoccus vitulinus	strain=DSM 15615	GCA_002902265.1	71237	71237	type	True	81.2649	469	750	95	below_threshold
Mammaliicoccus sciuri	strain=NCTC12103	GCA_900474615.1	1296	1296	type	True	81.1699	520	750	95	below_threshold
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	81.1495	513	750	95	below_threshold
Mammaliicoccus vitulinus	strain=FDAARGOS_1207	GCA_016889245.1	71237	71237	suspected-type	True	81.1483	491	750	95	below_threshold
Mammaliicoccus lentus	strain=NCTC 12102	GCA_002902755.1	42858	42858	type	True	81.0654	474	750	95	below_threshold
Mammaliicoccus lentus	strain=NCTC12102	GCA_900458735.1	42858	42858	type	True	81.0606	484	750	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	78.0625	111	750	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	77.5769	133	750	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	77.4518	130	750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:46,758] [INFO] DFAST Taxonomy check result was written to GCF_002902525.1_ASM290252v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:46,759] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:46,759] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:46,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb79170e-32d2-4245-8590-c0a6659d55fd/dqc_reference/checkm_data
[2024-01-24 12:31:46,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:46,784] [INFO] Task started: CheckM
[2024-01-24 12:31:46,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902525.1_ASM290252v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902525.1_ASM290252v1_genomic.fna/checkm_input GCF_002902525.1_ASM290252v1_genomic.fna/checkm_result
[2024-01-24 12:32:05,319] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:05,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:05,338] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:05,338] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:05,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902525.1_ASM290252v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:05,339] [INFO] Task started: Blastn
[2024-01-24 12:32:05,339] [INFO] Running command: blastn -query GCF_002902525.1_ASM290252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb79170e-32d2-4245-8590-c0a6659d55fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902525.1_ASM290252v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:06,042] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:06,045] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:06,045] [INFO] Target genome list was writen to GCF_002902525.1_ASM290252v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:06,050] [INFO] Task started: fastANI
[2024-01-24 12:32:06,050] [INFO] Running command: fastANI --query /var/lib/cwl/stga6c388db-9776-4923-a9d9-e2a4508ef2f3/GCF_002902525.1_ASM290252v1_genomic.fna.gz --refList GCF_002902525.1_ASM290252v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902525.1_ASM290252v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:10,676] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:10,684] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:10,684] [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_002902525.1	s__Mammaliicoccus stepanovicii	100.0	748	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	100.00	100.00	1.00	0.99	3	conclusive
GCF_003970575.1	s__Mammaliicoccus fleurettii	81.5782	480	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.35	98.97	0.91	0.88	9	-
GCF_002902265.1	s__Mammaliicoccus vitulinus	81.2416	471	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	98.82	98.52	0.92	0.85	19	-
GCF_002901825.1	s__Mammaliicoccus sciuri	81.2287	505	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
GCF_002902755.1	s__Mammaliicoccus lentus	81.0654	474	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.03	97.66	0.94	0.90	21	-
GCF_002732165.1	s__Staphylococcus xylosus	77.9111	144	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_000816085.1	s__Staphylococcus hyicus	77.7871	107	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
GCF_006094395.1	s__Staphylococcus haemolyticus	77.5353	145	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_003815035.1	s__Abyssicoccus albus	77.058	57	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__DSM-29158;g__Abyssicoccus	95.0	98.05	98.05	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:10,687] [INFO] GTDB search result was written to GCF_002902525.1_ASM290252v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:10,688] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:10,692] [INFO] DFAST_QC result json was written to GCF_002902525.1_ASM290252v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:10,692] [INFO] DFAST_QC completed!
[2024-01-24 12:32:10,692] [INFO] Total running time: 0h0m38s