[2024-01-25 18:14:50,552] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:50,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:50,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg04d305fc-b827-45de-b292-688ca8dd4700/dqc_reference
[2024-01-25 18:14:51,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:51,665] [INFO] Task started: Prodigal
[2024-01-25 18:14:51,666] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2022545-4f28-4d2e-b19f-d05e076db49b/GCF_003970495.1_ASM397049v1_genomic.fna.gz | prodigal -d GCF_003970495.1_ASM397049v1_genomic.fna/cds.fna -a GCF_003970495.1_ASM397049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:55,126] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:55,126] [INFO] Task started: HMMsearch
[2024-01-25 18:14:55,126] [INFO] Running command: hmmsearch --tblout GCF_003970495.1_ASM397049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04d305fc-b827-45de-b292-688ca8dd4700/dqc_reference/reference_markers.hmm GCF_003970495.1_ASM397049v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:55,322] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:55,323] [INFO] Found 6/6 markers.
[2024-01-25 18:14:55,343] [INFO] Query marker FASTA was written to GCF_003970495.1_ASM397049v1_genomic.fna/markers.fasta
[2024-01-25 18:14:55,343] [INFO] Task started: Blastn
[2024-01-25 18:14:55,343] [INFO] Running command: blastn -query GCF_003970495.1_ASM397049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04d305fc-b827-45de-b292-688ca8dd4700/dqc_reference/reference_markers.fasta -out GCF_003970495.1_ASM397049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:55,932] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:55,935] [INFO] Selected 20 target genomes.
[2024-01-25 18:14:55,936] [INFO] Target genome list was writen to GCF_003970495.1_ASM397049v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:55,948] [INFO] Task started: fastANI
[2024-01-25 18:14:55,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2022545-4f28-4d2e-b19f-d05e076db49b/GCF_003970495.1_ASM397049v1_genomic.fna.gz --refList GCF_003970495.1_ASM397049v1_genomic.fna/target_genomes.txt --output GCF_003970495.1_ASM397049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:05,002] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:05,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04d305fc-b827-45de-b292-688ca8dd4700/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:05,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04d305fc-b827-45de-b292-688ca8dd4700/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:05,015] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:05,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:05,015] [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 pasteuri	strain=DSM 10656	GCA_003970495.1	45972	45972	type	True	100.0	770	777	95	conclusive
Staphylococcus warneri	strain=NCTC 11044	GCA_002901765.1	1292	1292	type	True	84.6504	617	777	95	below_threshold
Staphylococcus warneri	strain=NCTC11044	GCA_900636385.1	1292	1292	type	True	84.5803	630	777	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=NCTC 11045	GCA_002902325.1	72758	29388	type	True	80.4911	418	777	95	below_threshold
Staphylococcus capitis	strain=NCTC11045	GCA_901482635.1	29388	29388	type	True	80.3888	434	777	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	80.3888	434	777	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	80.0192	378	777	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC11042	GCA_900458595.1	1283	1283	type	True	79.9501	363	777	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.9422	372	777	95	below_threshold
Staphylococcus haemolyticus	strain=ATCC 29970	GCA_006094395.1	1283	1283	type	True	79.9082	366	777	95	below_threshold
Staphylococcus croceilyticus	strain=CCM 8421	GCA_004684875.1	319942	319942	type	True	79.9072	370	777	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC 11042	GCA_002901805.1	1283	1283	type	True	79.9048	364	777	95	below_threshold
Staphylococcus croceilyticus	strain=CCUG 62728	GCA_002902575.1	319942	319942	type	True	79.8711	359	777	95	below_threshold
Staphylococcus caledonicus	strain=H8/1	GCA_016238465.1	2741333	2741333	type	True	79.8299	355	777	95	below_threshold
Staphylococcus pragensis	strain=CCM 8529	GCA_004785665.1	1611836	1611836	type	True	79.7528	375	777	95	below_threshold
Staphylococcus pragensis	strain=CCM 8529	GCA_014635505.1	1611836	1611836	type	True	79.6992	373	777	95	below_threshold
Staphylococcus devriesei	strain=CCUG 58238	GCA_002902625.1	586733	586733	type	True	79.6704	353	777	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.3608	359	777	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	79.1709	370	777	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	78.5749	291	777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:05,017] [INFO] DFAST Taxonomy check result was written to GCF_003970495.1_ASM397049v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:05,017] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:05,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:05,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04d305fc-b827-45de-b292-688ca8dd4700/dqc_reference/checkm_data
[2024-01-25 18:15:05,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:05,046] [INFO] Task started: CheckM
[2024-01-25 18:15:05,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970495.1_ASM397049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970495.1_ASM397049v1_genomic.fna/checkm_input GCF_003970495.1_ASM397049v1_genomic.fna/checkm_result
[2024-01-25 18:15:22,022] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:22,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:22,041] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:22,041] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:22,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970495.1_ASM397049v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:22,042] [INFO] Task started: Blastn
[2024-01-25 18:15:22,042] [INFO] Running command: blastn -query GCF_003970495.1_ASM397049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04d305fc-b827-45de-b292-688ca8dd4700/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970495.1_ASM397049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:22,845] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:22,848] [INFO] Selected 13 target genomes.
[2024-01-25 18:15:22,848] [INFO] Target genome list was writen to GCF_003970495.1_ASM397049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:22,858] [INFO] Task started: fastANI
[2024-01-25 18:15:22,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2022545-4f28-4d2e-b19f-d05e076db49b/GCF_003970495.1_ASM397049v1_genomic.fna.gz --refList GCF_003970495.1_ASM397049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970495.1_ASM397049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:29,853] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:29,861] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:29,862] [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_003970495.1	s__Staphylococcus pasteuri	100.0	770	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	conclusive
GCF_900636385.1	s__Staphylococcus warneri	84.5803	630	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_003491325.1	s__Staphylococcus warneri_A	84.3228	629	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_002902325.1	s__Staphylococcus capitis	80.5055	417	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
GCF_002902725.1	s__Staphylococcus caprae	80.2228	439	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_002902565.1	s__Staphylococcus petrasii	80.0341	377	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_006094395.1	s__Staphylococcus haemolyticus	79.9412	366	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCA_002902575.1	s__Staphylococcus croceilyticus	79.8806	359	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_003035445.1	s__Staphylococcus devriesei_A	79.7952	370	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCF_004785665.1	s__Staphylococcus pragensis	79.7671	374	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_002902625.1	s__Staphylococcus devriesei	79.6704	353	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
GCF_015025035.1	s__Staphylococcus sp015025035	79.5191	370	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
GCF_002902405.1	s__Staphylococcus schweitzeri	79.4679	368	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:29,863] [INFO] GTDB search result was written to GCF_003970495.1_ASM397049v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:29,864] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:29,867] [INFO] DFAST_QC result json was written to GCF_003970495.1_ASM397049v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:29,867] [INFO] DFAST_QC completed!
[2024-01-25 18:15:29,867] [INFO] Total running time: 0h0m39s