[2024-01-24 13:31:12,018] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,019] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg46fe1c3b-e540-40a7-9516-9bd7b6bd1a63/dqc_reference
[2024-01-24 13:31:13,218] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,219] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,219] [INFO] Running command: gunzip -c /var/lib/cwl/stg09520629-dff7-45f1-8bb2-78f772c7efd1/GCF_900474585.1_41315_E01_genomic.fna.gz | prodigal -d GCF_900474585.1_41315_E01_genomic.fna/cds.fna -a GCF_900474585.1_41315_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:18,158] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:18,158] [INFO] Task started: HMMsearch
[2024-01-24 13:31:18,158] [INFO] Running command: hmmsearch --tblout GCF_900474585.1_41315_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46fe1c3b-e540-40a7-9516-9bd7b6bd1a63/dqc_reference/reference_markers.hmm GCF_900474585.1_41315_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:18,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:18,355] [INFO] Found 6/6 markers.
[2024-01-24 13:31:18,377] [INFO] Query marker FASTA was written to GCF_900474585.1_41315_E01_genomic.fna/markers.fasta
[2024-01-24 13:31:18,377] [INFO] Task started: Blastn
[2024-01-24 13:31:18,377] [INFO] Running command: blastn -query GCF_900474585.1_41315_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg46fe1c3b-e540-40a7-9516-9bd7b6bd1a63/dqc_reference/reference_markers.fasta -out GCF_900474585.1_41315_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:18,962] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:18,966] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:18,967] [INFO] Target genome list was writen to GCF_900474585.1_41315_E01_genomic.fna/target_genomes.txt
[2024-01-24 13:31:18,973] [INFO] Task started: fastANI
[2024-01-24 13:31:18,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg09520629-dff7-45f1-8bb2-78f772c7efd1/GCF_900474585.1_41315_E01_genomic.fna.gz --refList GCF_900474585.1_41315_E01_genomic.fna/target_genomes.txt --output GCF_900474585.1_41315_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:24,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:24,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46fe1c3b-e540-40a7-9516-9bd7b6bd1a63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:24,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46fe1c3b-e540-40a7-9516-9bd7b6bd1a63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:24,565] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:31:24,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:24,565] [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=NCTC10350	GCA_900474585.1	1284	1284	type	True	100.0	824	824	95	conclusive
Staphylococcus hyicus	strain=ATCC 11249	GCA_000816085.1	1284	1284	type	True	100.0	824	824	95	conclusive
Staphylococcus hyicus	strain=CCUG 6509	GCA_003970475.1	1284	1284	type	True	99.9528	782	824	95	conclusive
Staphylococcus agnetis	strain=DSM 23656	GCA_002901865.1	985762	985762	type	True	86.7031	655	824	95	below_threshold
Staphylococcus chromogenes	strain=NCTC10530	GCA_900458195.1	46126	46126	type	True	81.5165	487	824	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	78.9763	167	824	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	78.9743	236	824	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	77.8065	161	824	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:24,567] [INFO] DFAST Taxonomy check result was written to GCF_900474585.1_41315_E01_genomic.fna/tc_result.tsv
[2024-01-24 13:31:24,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:24,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:24,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46fe1c3b-e540-40a7-9516-9bd7b6bd1a63/dqc_reference/checkm_data
[2024-01-24 13:31:24,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:24,596] [INFO] Task started: CheckM
[2024-01-24 13:31:24,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900474585.1_41315_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900474585.1_41315_E01_genomic.fna/checkm_input GCF_900474585.1_41315_E01_genomic.fna/checkm_result
[2024-01-24 13:31:45,526] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:45,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:45,547] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:45,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:45,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900474585.1_41315_E01_genomic.fna/markers.fasta)
[2024-01-24 13:31:45,548] [INFO] Task started: Blastn
[2024-01-24 13:31:45,548] [INFO] Running command: blastn -query GCF_900474585.1_41315_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg46fe1c3b-e540-40a7-9516-9bd7b6bd1a63/dqc_reference/reference_markers_gtdb.fasta -out GCF_900474585.1_41315_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:46,294] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:46,300] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:46,300] [INFO] Target genome list was writen to GCF_900474585.1_41315_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:46,308] [INFO] Task started: fastANI
[2024-01-24 13:31:46,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg09520629-dff7-45f1-8bb2-78f772c7efd1/GCF_900474585.1_41315_E01_genomic.fna.gz --refList GCF_900474585.1_41315_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900474585.1_41315_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:51,894] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:51,904] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:51,905] [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	100.0	824	824	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	86.6833	655	824	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	81.2831	454	824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.79	96.35	0.95	0.90	130	-
GCF_900636325.1	s__Staphylococcus delphini	79.7112	236	824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_010365305.1	s__Staphylococcus sp010365305	79.2474	256	824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902385.1	s__Staphylococcus intermedius	79.1596	242	824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_900183575.1	s__Staphylococcus cornubiensis	79.1552	271	824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900458895.2	s__Staphylococcus schleiferi	79.1275	274	824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_002901995.1	s__Staphylococcus coagulans	78.9679	250	824	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCF_002902565.1	s__Staphylococcus petrasii	77.8065	161	824	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	77.419	137	824	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	77.3212	164	824	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 13:31:51,906] [INFO] GTDB search result was written to GCF_900474585.1_41315_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:51,907] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:51,910] [INFO] DFAST_QC result json was written to GCF_900474585.1_41315_E01_genomic.fna/dqc_result.json
[2024-01-24 13:31:51,910] [INFO] DFAST_QC completed!
[2024-01-24 13:31:51,910] [INFO] Total running time: 0h0m40s