[2024-01-24 14:22:04,574] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b009290-5fd2-448e-bd1f-80fd415c687c/dqc_reference
[2024-01-24 14:22:05,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,884] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgadb98d06-ff97-4654-b39c-f356985f0386/GCF_003970475.1_ASM397047v1_genomic.fna.gz | prodigal -d GCF_003970475.1_ASM397047v1_genomic.fna/cds.fna -a GCF_003970475.1_ASM397047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:11,057] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:11,057] [INFO] Task started: HMMsearch
[2024-01-24 14:22:11,057] [INFO] Running command: hmmsearch --tblout GCF_003970475.1_ASM397047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b009290-5fd2-448e-bd1f-80fd415c687c/dqc_reference/reference_markers.hmm GCF_003970475.1_ASM397047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:11,334] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:11,336] [INFO] Found 6/6 markers.
[2024-01-24 14:22:11,362] [INFO] Query marker FASTA was written to GCF_003970475.1_ASM397047v1_genomic.fna/markers.fasta
[2024-01-24 14:22:11,362] [INFO] Task started: Blastn
[2024-01-24 14:22:11,362] [INFO] Running command: blastn -query GCF_003970475.1_ASM397047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b009290-5fd2-448e-bd1f-80fd415c687c/dqc_reference/reference_markers.fasta -out GCF_003970475.1_ASM397047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:12,032] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:12,036] [INFO] Selected 12 target genomes.
[2024-01-24 14:22:12,037] [INFO] Target genome list was writen to GCF_003970475.1_ASM397047v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:12,045] [INFO] Task started: fastANI
[2024-01-24 14:22:12,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb98d06-ff97-4654-b39c-f356985f0386/GCF_003970475.1_ASM397047v1_genomic.fna.gz --refList GCF_003970475.1_ASM397047v1_genomic.fna/target_genomes.txt --output GCF_003970475.1_ASM397047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:18,379] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:18,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b009290-5fd2-448e-bd1f-80fd415c687c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:18,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b009290-5fd2-448e-bd1f-80fd415c687c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:18,392] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:22:18,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:18,392] [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 hyicus	strain=CCUG 6509	GCA_003970475.1	1284	1284	type	True	100.0	785	786	95	conclusive
Staphylococcus hyicus	strain=ATCC 11249	GCA_000816085.1	1284	1284	type	True	99.9983	785	786	95	conclusive
Staphylococcus hyicus	strain=NCTC10350	GCA_900474585.1	1284	1284	type	True	99.9982	785	786	95	conclusive
Staphylococcus agnetis	strain=DSM 23656	GCA_002901865.1	985762	985762	type	True	86.7897	621	786	95	below_threshold
Staphylococcus chromogenes	strain=NCTC10530	GCA_900458195.1	46126	46126	type	True	81.2163	456	786	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	78.7465	230	786	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	77.8767	152	786	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	77.713	153	786	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:18,394] [INFO] DFAST Taxonomy check result was written to GCF_003970475.1_ASM397047v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:18,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:18,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:18,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b009290-5fd2-448e-bd1f-80fd415c687c/dqc_reference/checkm_data
[2024-01-24 14:22:18,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:18,427] [INFO] Task started: CheckM
[2024-01-24 14:22:18,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970475.1_ASM397047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970475.1_ASM397047v1_genomic.fna/checkm_input GCF_003970475.1_ASM397047v1_genomic.fna/checkm_result
[2024-01-24 14:22:41,060] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:41,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:41,083] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:41,083] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:41,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970475.1_ASM397047v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:41,084] [INFO] Task started: Blastn
[2024-01-24 14:22:41,084] [INFO] Running command: blastn -query GCF_003970475.1_ASM397047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b009290-5fd2-448e-bd1f-80fd415c687c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970475.1_ASM397047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:41,873] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:41,876] [INFO] Selected 12 target genomes.
[2024-01-24 14:22:41,876] [INFO] Target genome list was writen to GCF_003970475.1_ASM397047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:41,892] [INFO] Task started: fastANI
[2024-01-24 14:22:41,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb98d06-ff97-4654-b39c-f356985f0386/GCF_003970475.1_ASM397047v1_genomic.fna.gz --refList GCF_003970475.1_ASM397047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970475.1_ASM397047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:47,474] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:47,488] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:47,489] [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_000816085.1	s__Staphylococcus hyicus	99.9983	785	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	conclusive
GCF_002901865.1	s__Staphylococcus agnetis	86.806	620	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCF_002901945.1	s__Staphylococcus chromogenes	81.2725	453	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.79	96.35	0.95	0.90	130	-
GCF_900183575.1	s__Staphylococcus cornubiensis	79.0279	254	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636325.1	s__Staphylococcus delphini	78.9104	230	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_002902385.1	s__Staphylococcus intermedius	78.825	236	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_010365305.1	s__Staphylococcus sp010365305	78.8112	243	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901995.1	s__Staphylococcus coagulans	78.602	258	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCA_900458895.2	s__Staphylococcus schleiferi	78.4801	256	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_002902565.1	s__Staphylococcus petrasii	77.8998	151	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_002901825.1	s__Mammaliicoccus sciuri	77.3841	123	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
GCF_014635045.1	s__Staphylococcus nepalensis	77.1189	157	786	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.49	99.27	0.96	0.93	23	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:47,493] [INFO] GTDB search result was written to GCF_003970475.1_ASM397047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:47,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:47,497] [INFO] DFAST_QC result json was written to GCF_003970475.1_ASM397047v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:47,497] [INFO] DFAST_QC completed!
[2024-01-24 14:22:47,497] [INFO] Total running time: 0h0m43s