[2024-01-24 14:19:35,060] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:35,067] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:35,067] [INFO] DQC Reference Directory: /var/lib/cwl/stgebf1e664-1e23-45f2-8b8a-73cfd931c455/dqc_reference
[2024-01-24 14:19:36,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:36,523] [INFO] Task started: Prodigal
[2024-01-24 14:19:36,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg92527196-4133-4d6f-8875-cd6ace49de88/GCF_002901845.1_ASM290184v1_genomic.fna.gz | prodigal -d GCF_002901845.1_ASM290184v1_genomic.fna/cds.fna -a GCF_002901845.1_ASM290184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:40,668] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:40,668] [INFO] Task started: HMMsearch
[2024-01-24 14:19:40,668] [INFO] Running command: hmmsearch --tblout GCF_002901845.1_ASM290184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebf1e664-1e23-45f2-8b8a-73cfd931c455/dqc_reference/reference_markers.hmm GCF_002901845.1_ASM290184v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:41,041] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:41,042] [INFO] Found 6/6 markers.
[2024-01-24 14:19:41,079] [INFO] Query marker FASTA was written to GCF_002901845.1_ASM290184v1_genomic.fna/markers.fasta
[2024-01-24 14:19:41,079] [INFO] Task started: Blastn
[2024-01-24 14:19:41,080] [INFO] Running command: blastn -query GCF_002901845.1_ASM290184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebf1e664-1e23-45f2-8b8a-73cfd931c455/dqc_reference/reference_markers.fasta -out GCF_002901845.1_ASM290184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:41,746] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:41,750] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:41,750] [INFO] Target genome list was writen to GCF_002901845.1_ASM290184v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:41,785] [INFO] Task started: fastANI
[2024-01-24 14:19:41,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg92527196-4133-4d6f-8875-cd6ace49de88/GCF_002901845.1_ASM290184v1_genomic.fna.gz --refList GCF_002901845.1_ASM290184v1_genomic.fna/target_genomes.txt --output GCF_002901845.1_ASM290184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:48,398] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:48,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebf1e664-1e23-45f2-8b8a-73cfd931c455/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:48,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebf1e664-1e23-45f2-8b8a-73cfd931c455/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:48,412] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:19:48,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:48,412] [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 hominis subsp. hominis	strain=NCTC 11320	GCA_002901845.1	145391	1290	type	True	100.0	723	724	95	conclusive
Staphylococcus hominis	strain=NCTC 11320	GCA_900458635.1	1290	1290	type	True	99.9944	722	724	95	conclusive
Staphylococcus hominis subsp. novobiosepticus	strain=CCUG 42399	GCA_002902465.1	145393	1290	type	True	97.3343	620	724	95	conclusive
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	81.5604	465	724	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	81.5532	494	724	95	below_threshold
Staphylococcus pragensis	strain=CCM 8529	GCA_004785665.1	1611836	1611836	type	True	81.353	493	724	95	below_threshold
Staphylococcus pragensis	strain=CCM 8529	GCA_014635505.1	1611836	1611836	type	True	81.3328	488	724	95	below_threshold
Staphylococcus croceilyticus	strain=CCUG 62728	GCA_002902575.1	319942	319942	type	True	81.1356	465	724	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	81.0886	472	724	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	79.0893	312	724	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.0804	309	724	95	below_threshold
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	77.6711	179	724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:48,414] [INFO] DFAST Taxonomy check result was written to GCF_002901845.1_ASM290184v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:48,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:48,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:48,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebf1e664-1e23-45f2-8b8a-73cfd931c455/dqc_reference/checkm_data
[2024-01-24 14:19:48,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:48,443] [INFO] Task started: CheckM
[2024-01-24 14:19:48,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002901845.1_ASM290184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002901845.1_ASM290184v1_genomic.fna/checkm_input GCF_002901845.1_ASM290184v1_genomic.fna/checkm_result
[2024-01-24 14:20:09,100] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:09,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:09,122] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:09,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:09,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002901845.1_ASM290184v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:09,123] [INFO] Task started: Blastn
[2024-01-24 14:20:09,123] [INFO] Running command: blastn -query GCF_002901845.1_ASM290184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebf1e664-1e23-45f2-8b8a-73cfd931c455/dqc_reference/reference_markers_gtdb.fasta -out GCF_002901845.1_ASM290184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:09,989] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:09,992] [INFO] Selected 9 target genomes.
[2024-01-24 14:20:09,992] [INFO] Target genome list was writen to GCF_002901845.1_ASM290184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:10,013] [INFO] Task started: fastANI
[2024-01-24 14:20:10,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg92527196-4133-4d6f-8875-cd6ace49de88/GCF_002901845.1_ASM290184v1_genomic.fna.gz --refList GCF_002901845.1_ASM290184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002901845.1_ASM290184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:14,953] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:14,962] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:14,962] [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_002901845.1	s__Staphylococcus hominis	100.0	723	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	conclusive
GCF_002902565.1	s__Staphylococcus petrasii	81.5604	465	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_004785665.1	s__Staphylococcus pragensis	81.3713	492	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCA_002902575.1	s__Staphylococcus croceilyticus	81.1356	465	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_006094395.1	s__Staphylococcus haemolyticus	81.085	466	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_001224225.1	s__Staphylococcus borealis	81.0324	468	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_003035445.1	s__Staphylococcus devriesei_A	80.7832	461	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCF_002902625.1	s__Staphylococcus devriesei	80.5808	439	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
GCF_002901705.1	s__Staphylococcus lugdunensis	79.3164	313	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.51	99.34	0.98	0.96	70	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:14,964] [INFO] GTDB search result was written to GCF_002901845.1_ASM290184v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:14,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:14,968] [INFO] DFAST_QC result json was written to GCF_002901845.1_ASM290184v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:14,969] [INFO] DFAST_QC completed!
[2024-01-24 14:20:14,969] [INFO] Total running time: 0h0m40s