[2024-01-24 12:22:48,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,324] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,324] [INFO] DQC Reference Directory: /var/lib/cwl/stgde4e1028-c22d-4198-b1eb-314878f6810f/dqc_reference
[2024-01-24 12:22:49,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,627] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg80dac3ca-1612-4b0e-9aeb-4d6f4c605dfb/GCF_002902705.1_ASM290270v1_genomic.fna.gz | prodigal -d GCF_002902705.1_ASM290270v1_genomic.fna/cds.fna -a GCF_002902705.1_ASM290270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:53,728] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:53,729] [INFO] Task started: HMMsearch
[2024-01-24 12:22:53,729] [INFO] Running command: hmmsearch --tblout GCF_002902705.1_ASM290270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde4e1028-c22d-4198-b1eb-314878f6810f/dqc_reference/reference_markers.hmm GCF_002902705.1_ASM290270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:53,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:53,942] [INFO] Found 6/6 markers.
[2024-01-24 12:22:53,965] [INFO] Query marker FASTA was written to GCF_002902705.1_ASM290270v1_genomic.fna/markers.fasta
[2024-01-24 12:22:53,966] [INFO] Task started: Blastn
[2024-01-24 12:22:53,966] [INFO] Running command: blastn -query GCF_002902705.1_ASM290270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde4e1028-c22d-4198-b1eb-314878f6810f/dqc_reference/reference_markers.fasta -out GCF_002902705.1_ASM290270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:54,592] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:54,595] [INFO] Selected 24 target genomes.
[2024-01-24 12:22:54,596] [INFO] Target genome list was writen to GCF_002902705.1_ASM290270v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:54,603] [INFO] Task started: fastANI
[2024-01-24 12:22:54,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg80dac3ca-1612-4b0e-9aeb-4d6f4c605dfb/GCF_002902705.1_ASM290270v1_genomic.fna.gz --refList GCF_002902705.1_ASM290270v1_genomic.fna/target_genomes.txt --output GCF_002902705.1_ASM290270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:05,575] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:05,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde4e1028-c22d-4198-b1eb-314878f6810f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:05,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde4e1028-c22d-4198-b1eb-314878f6810f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:05,593] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:05,593] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:05,593] [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
Staphylococcus massiliensis	strain=CCUG 55927	GCA_002902705.1	555791	555791	type	True	100.0	686	688	95	conclusive
Staphylococcus massiliensis	strain=CCUG 55927	GCA_000298075.1	555791	555791	type	True	99.9779	684	688	95	conclusive
Staphylococcus simulans	strain=NCTC 11046	GCA_002902285.1	1286	1286	type	True	78.9263	179	688	95	below_threshold
Staphylococcus simulans	strain=NCTC11046	GCA_900474685.1	1286	1286	type	True	78.889	177	688	95	below_threshold
Staphylococcus cornubiensis	strain=NW1	GCA_900183575.1	1986155	1986155	type	True	78.5844	156	688	95	below_threshold
Staphylococcus cohnii subsp. barensis	strain=SC5	GCA_014180735.1	2834574	29382	type	True	78.5383	142	688	95	below_threshold
Staphylococcus pettenkoferi	strain=FDAARGOS_1071	GCA_016127935.1	170573	170573	type	True	78.5041	154	688	95	below_threshold
Staphylococcus borealis	strain=51-48	GCA_013345165.1	2742203	2742203	type	True	78.4687	176	688	95	below_threshold
Staphylococcus borealis	strain=51-48	GCA_001224225.1	2742203	2742203	type	True	78.4581	174	688	95	below_threshold
Staphylococcus ureilyticus	strain=DSM 6718	GCA_002902235.1	94138	94138	type	True	78.3872	142	688	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=NCTC 11045	GCA_002902325.1	72758	29388	type	True	78.3774	174	688	95	below_threshold
Staphylococcus capitis subsp. urealyticus	strain=DSM 6717	GCA_002901925.1	74703	29388	type	True	78.3533	158	688	95	below_threshold
Staphylococcus delphini	strain=NCTC12225	GCA_900636325.1	53344	53344	type	True	78.2927	144	688	95	below_threshold
Staphylococcus pettenkoferi	strain=CCUG 51270	GCA_002902685.1	170573	170573	type	True	78.2834	151	688	95	below_threshold
Staphylococcus delphini	strain=NCTC 12225	GCA_002902785.1	53344	53344	type	True	78.2337	141	688	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	78.1926	161	688	95	below_threshold
Staphylococcus pasteuri	strain=DSM 10656	GCA_003970495.1	45972	45972	type	True	78.1388	165	688	95	below_threshold
Staphylococcus simiae	strain=NCTC13838	GCA_900187055.1	308354	308354	type	True	77.8534	178	688	95	below_threshold
Staphylococcus simiae	strain=CCM 7213	GCA_000235645.2	308354	308354	type	True	77.5669	165	688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:05,595] [INFO] DFAST Taxonomy check result was written to GCF_002902705.1_ASM290270v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:05,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:05,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:05,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde4e1028-c22d-4198-b1eb-314878f6810f/dqc_reference/checkm_data
[2024-01-24 12:23:05,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:05,628] [INFO] Task started: CheckM
[2024-01-24 12:23:05,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902705.1_ASM290270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902705.1_ASM290270v1_genomic.fna/checkm_input GCF_002902705.1_ASM290270v1_genomic.fna/checkm_result
[2024-01-24 12:23:25,181] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:25,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,199] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:25,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:25,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902705.1_ASM290270v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:25,200] [INFO] Task started: Blastn
[2024-01-24 12:23:25,200] [INFO] Running command: blastn -query GCF_002902705.1_ASM290270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde4e1028-c22d-4198-b1eb-314878f6810f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902705.1_ASM290270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:26,028] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:26,032] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:26,032] [INFO] Target genome list was writen to GCF_002902705.1_ASM290270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:26,056] [INFO] Task started: fastANI
[2024-01-24 12:23:26,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg80dac3ca-1612-4b0e-9aeb-4d6f4c605dfb/GCF_002902705.1_ASM290270v1_genomic.fna.gz --refList GCF_002902705.1_ASM290270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902705.1_ASM290270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:36,020] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,040] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:36,040] [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_000298075.1	s__Staphylococcus massiliensis	99.9779	684	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.92	99.87	0.97	0.95	3	conclusive
GCF_002902285.1	s__Staphylococcus simulans	78.9373	178	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	-
GCF_003043455.1	s__Staphylococcus simulans_A	78.9029	177	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.25	98.25	0.90	0.90	2	-
GCF_900183575.1	s__Staphylococcus cornubiensis	78.5844	156	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	78.5266	134	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_010365305.1	s__Staphylococcus sp010365305	78.4997	139	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001224225.1	s__Staphylococcus borealis	78.4887	172	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_002902235.1	s__Staphylococcus ureilyticus	78.4151	141	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_002902325.1	s__Staphylococcus capitis	78.3774	174	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
GCF_002902685.1	s__Staphylococcus pettenkoferi	78.3094	150	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.48	96.01	0.95	0.89	21	-
GCF_002902365.1	s__Staphylococcus cohnii	78.3048	144	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
GCF_900636325.1	s__Staphylococcus delphini	78.2927	144	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_002902565.1	s__Staphylococcus petrasii	78.1615	191	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_003970495.1	s__Staphylococcus pasteuri	78.1388	165	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_002614725.1	s__Staphylococcus edaphicus	78.1371	137	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902345.1	s__Staphylococcus arlettae	78.1113	161	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.12	98.73	0.94	0.91	41	-
GCF_013391405.1	s__Staphylococcus sp013391405	78.0886	158	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357005.1	s__Staphylococcus simiae_A	77.9753	163	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.91	0.98	0.98	6	-
GCF_003012915.1	s__Staphylococcus felis	77.8952	120	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.05	98.64	0.95	0.91	31	-
GCF_900458815.1	s__Staphylococcus saccharolyticus	77.8781	143	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.11	97.94	0.98	0.95	15	-
GCF_002902085.1	s__Staphylococcus simiae	77.8017	176	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,043] [INFO] GTDB search result was written to GCF_002902705.1_ASM290270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:36,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:36,054] [INFO] DFAST_QC result json was written to GCF_002902705.1_ASM290270v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:36,055] [INFO] DFAST_QC completed!
[2024-01-24 12:23:36,055] [INFO] Total running time: 0h0m48s