[2024-01-24 14:19:00,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:00,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:00,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dc66b11-7836-4168-b0fe-ded5a91fe675/dqc_reference
[2024-01-24 14:19:02,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,419] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b30cbfd-5144-4caf-af68-200799b3a228/GCF_900458385.1_35910_C02_genomic.fna.gz | prodigal -d GCF_900458385.1_35910_C02_genomic.fna/cds.fna -a GCF_900458385.1_35910_C02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:07,670] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:07,671] [INFO] Task started: HMMsearch
[2024-01-24 14:19:07,671] [INFO] Running command: hmmsearch --tblout GCF_900458385.1_35910_C02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dc66b11-7836-4168-b0fe-ded5a91fe675/dqc_reference/reference_markers.hmm GCF_900458385.1_35910_C02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:07,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:07,959] [INFO] Found 6/6 markers.
[2024-01-24 14:19:07,990] [INFO] Query marker FASTA was written to GCF_900458385.1_35910_C02_genomic.fna/markers.fasta
[2024-01-24 14:19:07,991] [INFO] Task started: Blastn
[2024-01-24 14:19:07,991] [INFO] Running command: blastn -query GCF_900458385.1_35910_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dc66b11-7836-4168-b0fe-ded5a91fe675/dqc_reference/reference_markers.fasta -out GCF_900458385.1_35910_C02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:08,709] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:08,713] [INFO] Selected 12 target genomes.
[2024-01-24 14:19:08,713] [INFO] Target genome list was writen to GCF_900458385.1_35910_C02_genomic.fna/target_genomes.txt
[2024-01-24 14:19:08,722] [INFO] Task started: fastANI
[2024-01-24 14:19:08,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b30cbfd-5144-4caf-af68-200799b3a228/GCF_900458385.1_35910_C02_genomic.fna.gz --refList GCF_900458385.1_35910_C02_genomic.fna/target_genomes.txt --output GCF_900458385.1_35910_C02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:15,845] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:15,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dc66b11-7836-4168-b0fe-ded5a91fe675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:15,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dc66b11-7836-4168-b0fe-ded5a91fe675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:15,856] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:15,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:15,857] [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 caprae	strain=NCTC12196	GCA_900458385.1	29380	29380	type	True	100.0	879	881	95	conclusive
Staphylococcus caprae	strain=NCTC 12196	GCA_002902725.1	29380	29380	type	True	99.9136	819	881	95	conclusive
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	84.4237	689	881	95	below_threshold
Staphylococcus capitis	strain=NCTC11045	GCA_901482635.1	29388	29388	type	True	84.4033	686	881	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=NCTC 11045	GCA_002902325.1	72758	29388	type	True	84.174	673	881	95	below_threshold
Staphylococcus capitis subsp. urealyticus	strain=DSM 6717	GCA_002901925.1	74703	29388	type	True	84.1733	655	881	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	80.0107	400	881	95	below_threshold
Staphylococcus croceilyticus	strain=CCM 8421	GCA_004684875.1	319942	319942	type	True	79.8985	390	881	95	below_threshold
Staphylococcus croceilyticus	strain=CCUG 62728	GCA_002902575.1	319942	319942	type	True	79.866	379	881	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.6188	358	881	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	79.279	350	881	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	78.4721	267	881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:15,858] [INFO] DFAST Taxonomy check result was written to GCF_900458385.1_35910_C02_genomic.fna/tc_result.tsv
[2024-01-24 14:19:15,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:15,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:15,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dc66b11-7836-4168-b0fe-ded5a91fe675/dqc_reference/checkm_data
[2024-01-24 14:19:15,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:15,894] [INFO] Task started: CheckM
[2024-01-24 14:19:15,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900458385.1_35910_C02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900458385.1_35910_C02_genomic.fna/checkm_input GCF_900458385.1_35910_C02_genomic.fna/checkm_result
[2024-01-24 14:19:39,261] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:39,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:39,284] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:39,284] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:39,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900458385.1_35910_C02_genomic.fna/markers.fasta)
[2024-01-24 14:19:39,285] [INFO] Task started: Blastn
[2024-01-24 14:19:39,285] [INFO] Running command: blastn -query GCF_900458385.1_35910_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dc66b11-7836-4168-b0fe-ded5a91fe675/dqc_reference/reference_markers_gtdb.fasta -out GCF_900458385.1_35910_C02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:40,101] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:40,105] [INFO] Selected 12 target genomes.
[2024-01-24 14:19:40,105] [INFO] Target genome list was writen to GCF_900458385.1_35910_C02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:40,113] [INFO] Task started: fastANI
[2024-01-24 14:19:40,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b30cbfd-5144-4caf-af68-200799b3a228/GCF_900458385.1_35910_C02_genomic.fna.gz --refList GCF_900458385.1_35910_C02_genomic.fna/target_genomes_gtdb.txt --output GCF_900458385.1_35910_C02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:19:47,076] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:47,087] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:19:47,087] [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_002902725.1	s__Staphylococcus caprae	99.9136	819	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	conclusive
GCF_002902325.1	s__Staphylococcus capitis	84.2009	670	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
GCF_900458815.1	s__Staphylococcus saccharolyticus	81.8329	540	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.11	97.94	0.98	0.95	15	-
GCF_006742205.1	s__Staphylococcus epidermidis	80.9883	495	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.01	96.59	0.94	0.83	1079	-
GCF_900636385.1	s__Staphylococcus warneri	80.7746	459	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_006094395.1	s__Staphylococcus haemolyticus	80.4569	369	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_003970495.1	s__Staphylococcus pasteuri	80.2816	442	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_004785665.1	s__Staphylococcus pragensis	80.217	388	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_002902565.1	s__Staphylococcus petrasii	79.947	387	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCA_002902575.1	s__Staphylococcus croceilyticus	79.8522	380	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_001224225.1	s__Staphylococcus borealis	79.698	380	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_002901845.1	s__Staphylococcus hominis	79.275	354	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
--------------------------------------------------------------------------------
[2024-01-24 14:19:47,089] [INFO] GTDB search result was written to GCF_900458385.1_35910_C02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:19:47,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:19:47,093] [INFO] DFAST_QC result json was written to GCF_900458385.1_35910_C02_genomic.fna/dqc_result.json
[2024-01-24 14:19:47,093] [INFO] DFAST_QC completed!
[2024-01-24 14:19:47,093] [INFO] Total running time: 0h0m46s