[2024-01-25 18:53:06,344] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:06,346] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:06,346] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1926169-ece0-492c-ae13-a6fb4f0718d7/dqc_reference
[2024-01-25 18:53:07,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:07,523] [INFO] Task started: Prodigal
[2024-01-25 18:53:07,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c15d51b-c610-47bf-a719-00e938749be0/GCF_003968815.1_ASM396881v1_genomic.fna.gz | prodigal -d GCF_003968815.1_ASM396881v1_genomic.fna/cds.fna -a GCF_003968815.1_ASM396881v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:11,903] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:11,904] [INFO] Task started: HMMsearch
[2024-01-25 18:53:11,904] [INFO] Running command: hmmsearch --tblout GCF_003968815.1_ASM396881v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1926169-ece0-492c-ae13-a6fb4f0718d7/dqc_reference/reference_markers.hmm GCF_003968815.1_ASM396881v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:12,126] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:12,127] [INFO] Found 6/6 markers.
[2024-01-25 18:53:12,154] [INFO] Query marker FASTA was written to GCF_003968815.1_ASM396881v1_genomic.fna/markers.fasta
[2024-01-25 18:53:12,154] [INFO] Task started: Blastn
[2024-01-25 18:53:12,154] [INFO] Running command: blastn -query GCF_003968815.1_ASM396881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1926169-ece0-492c-ae13-a6fb4f0718d7/dqc_reference/reference_markers.fasta -out GCF_003968815.1_ASM396881v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:12,725] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:12,727] [INFO] Selected 21 target genomes.
[2024-01-25 18:53:12,727] [INFO] Target genome list was writen to GCF_003968815.1_ASM396881v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:12,740] [INFO] Task started: fastANI
[2024-01-25 18:53:12,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c15d51b-c610-47bf-a719-00e938749be0/GCF_003968815.1_ASM396881v1_genomic.fna.gz --refList GCF_003968815.1_ASM396881v1_genomic.fna/target_genomes.txt --output GCF_003968815.1_ASM396881v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:23,472] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:23,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1926169-ece0-492c-ae13-a6fb4f0718d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:23,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1926169-ece0-492c-ae13-a6fb4f0718d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:23,484] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:53:23,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:23,485] [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 gallinarum	strain=NCTC 12195	GCA_003968815.1	1293	1293	type	True	100.0	795	806	95	conclusive
Staphylococcus gallinarum	strain=DSM 20610	GCA_000875895.1	1293	1293	type	True	99.9691	787	806	95	conclusive
Staphylococcus equorum	strain=FDAARGOS_1149	GCA_016725305.1	246432	246432	type	True	80.5254	384	806	95	below_threshold
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_001006765.1	224030	61015	type	True	80.5179	422	806	95	below_threshold
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_002902045.1	224030	61015	type	True	80.5136	398	806	95	below_threshold
Staphylococcus xylosus	strain=NCTC11043	GCA_900458755.1	1288	1288	type	True	80.5011	389	806	95	below_threshold
Staphylococcus equorum	strain=NCTC12414	GCA_900458565.1	246432	246432	type	True	80.3812	391	806	95	below_threshold
Staphylococcus equorum subsp. linens	strain=DSM 15097	GCA_002901955.1	201829	246432	type	True	80.3488	373	806	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	80.3286	396	806	95	below_threshold
Staphylococcus equorum subsp. equorum	strain=NCTC 12414	GCA_003970515.1	29383	246432	type	True	80.3105	373	806	95	below_threshold
Staphylococcus caeli	strain=82B	GCA_900097965.1	2201815	2201815	type	True	80.2757	371	806	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	80.2612	384	806	95	below_threshold
Staphylococcus cohnii subsp. barensis	strain=SC5	GCA_014180735.1	2834574	29382	type	True	80.0293	369	806	95	below_threshold
Staphylococcus ureilyticus	strain=DSM 6718	GCA_002902235.1	94138	94138	type	True	79.7045	358	806	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	79.0236	234	806	95	below_threshold
Staphylococcus petrasii	strain=CCM 8418	GCA_004684865.1	1276936	1276936	type	True	78.9622	235	806	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	78.9599	226	806	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	78.9066	231	806	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	77.8953	73	806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:23,486] [INFO] DFAST Taxonomy check result was written to GCF_003968815.1_ASM396881v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:23,487] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:23,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:23,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1926169-ece0-492c-ae13-a6fb4f0718d7/dqc_reference/checkm_data
[2024-01-25 18:53:23,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:23,527] [INFO] Task started: CheckM
[2024-01-25 18:53:23,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003968815.1_ASM396881v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003968815.1_ASM396881v1_genomic.fna/checkm_input GCF_003968815.1_ASM396881v1_genomic.fna/checkm_result
[2024-01-25 18:53:42,717] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:42,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:42,732] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:42,732] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:42,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003968815.1_ASM396881v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:42,733] [INFO] Task started: Blastn
[2024-01-25 18:53:42,733] [INFO] Running command: blastn -query GCF_003968815.1_ASM396881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1926169-ece0-492c-ae13-a6fb4f0718d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003968815.1_ASM396881v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:43,475] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:43,478] [INFO] Selected 20 target genomes.
[2024-01-25 18:53:43,478] [INFO] Target genome list was writen to GCF_003968815.1_ASM396881v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:43,494] [INFO] Task started: fastANI
[2024-01-25 18:53:43,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c15d51b-c610-47bf-a719-00e938749be0/GCF_003968815.1_ASM396881v1_genomic.fna.gz --refList GCF_003968815.1_ASM396881v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003968815.1_ASM396881v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:54,474] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:54,494] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:54,494] [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_000875895.1	s__Staphylococcus gallinarum	99.9691	787	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.63	98.14	0.94	0.91	25	conclusive
GCF_001006765.1	s__Staphylococcus succinus	80.5179	422	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_002732165.1	s__Staphylococcus xylosus	80.4558	379	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_016774515.1	s__Staphylococcus xylosus_A	80.4227	398	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_900458565.1	s__Staphylococcus equorum	80.3812	391	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_900097965.1	s__Staphylococcus caeli	80.2912	370	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001747895.1	s__Staphylococcus equorum_A	80.2461	392	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	98.64	0.94	0.92	4	-
GCF_013391405.1	s__Staphylococcus sp013391405	80.2021	383	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010125.1	s__Staphylococcus saprophyticus	80.1754	373	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_002614725.1	s__Staphylococcus edaphicus	80.065	361	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338275.1	s__Staphylococcus xylosus_B	80.0596	411	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_001431205.1	s__Staphylococcus sp001431205	80.059	395	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902365.1	s__Staphylococcus cohnii	79.8143	365	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
GCF_002902235.1	s__Staphylococcus ureilyticus	79.7331	355	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_003019255.1	s__Staphylococcus kloosii	79.1423	309	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.99	96.08	0.96	0.89	9	-
GCF_003491325.1	s__Staphylococcus warneri_A	79.0045	248	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_002902565.1	s__Staphylococcus petrasii	78.9599	226	806	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	78.8827	240	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_004117835.1	s__Macrococcus_B sp004117835	77.7191	97	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:54,496] [INFO] GTDB search result was written to GCF_003968815.1_ASM396881v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:54,497] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:54,500] [INFO] DFAST_QC result json was written to GCF_003968815.1_ASM396881v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:54,500] [INFO] DFAST_QC completed!
[2024-01-25 18:53:54,500] [INFO] Total running time: 0h0m48s