[2024-01-24 13:40:30,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,169] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg71611588-452d-4e4d-b002-c07c9dfa8163/dqc_reference
[2024-01-24 13:40:31,476] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,477] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,477] [INFO] Running command: gunzip -c /var/lib/cwl/stgebb33825-bcbd-48fb-9632-4a901ac8ab60/GCF_002901905.1_ASM290190v1_genomic.fna.gz | prodigal -d GCF_002901905.1_ASM290190v1_genomic.fna/cds.fna -a GCF_002901905.1_ASM290190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:36,079] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:36,079] [INFO] Task started: HMMsearch
[2024-01-24 13:40:36,079] [INFO] Running command: hmmsearch --tblout GCF_002901905.1_ASM290190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71611588-452d-4e4d-b002-c07c9dfa8163/dqc_reference/reference_markers.hmm GCF_002901905.1_ASM290190v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:36,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:36,330] [INFO] Found 6/6 markers.
[2024-01-24 13:40:36,357] [INFO] Query marker FASTA was written to GCF_002901905.1_ASM290190v1_genomic.fna/markers.fasta
[2024-01-24 13:40:36,358] [INFO] Task started: Blastn
[2024-01-24 13:40:36,358] [INFO] Running command: blastn -query GCF_002901905.1_ASM290190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71611588-452d-4e4d-b002-c07c9dfa8163/dqc_reference/reference_markers.fasta -out GCF_002901905.1_ASM290190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:37,024] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:37,029] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:37,030] [INFO] Target genome list was writen to GCF_002901905.1_ASM290190v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:37,041] [INFO] Task started: fastANI
[2024-01-24 13:40:37,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb33825-bcbd-48fb-9632-4a901ac8ab60/GCF_002901905.1_ASM290190v1_genomic.fna.gz --refList GCF_002901905.1_ASM290190v1_genomic.fna/target_genomes.txt --output GCF_002901905.1_ASM290190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:43,613] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:43,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71611588-452d-4e4d-b002-c07c9dfa8163/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:43,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71611588-452d-4e4d-b002-c07c9dfa8163/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:43,620] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:40:43,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:43,620] [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 muscae	strain=DSM 7068	GCA_002901905.1	1294	1294	type	True	100.0	611	616	95	conclusive
Staphylococcus muscae	strain=NCTC13833	GCA_900187005.1	1294	1294	type	True	99.9942	615	616	95	conclusive
Staphylococcus muscae	strain=CCM 4175	GCA_014634965.1	1294	1294	type	True	99.9936	615	616	95	conclusive
Staphylococcus muscae	strain=ATCC 49910	GCA_003019275.1	1294	1294	type	True	99.9886	616	616	95	conclusive
Staphylococcus microti	strain=NCTC13832	GCA_900458705.1	569857	569857	type	True	81.8495	476	616	95	below_threshold
Staphylococcus rostri	strain=DSM 21968	GCA_002902145.1	522262	522262	type	True	81.751	462	616	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:43,622] [INFO] DFAST Taxonomy check result was written to GCF_002901905.1_ASM290190v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:43,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:43,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:43,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71611588-452d-4e4d-b002-c07c9dfa8163/dqc_reference/checkm_data
[2024-01-24 13:40:43,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:43,653] [INFO] Task started: CheckM
[2024-01-24 13:40:43,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002901905.1_ASM290190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002901905.1_ASM290190v1_genomic.fna/checkm_input GCF_002901905.1_ASM290190v1_genomic.fna/checkm_result
[2024-01-24 13:41:06,104] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:06,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:06,126] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:06,127] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:06,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002901905.1_ASM290190v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:06,128] [INFO] Task started: Blastn
[2024-01-24 13:41:06,128] [INFO] Running command: blastn -query GCF_002901905.1_ASM290190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71611588-452d-4e4d-b002-c07c9dfa8163/dqc_reference/reference_markers_gtdb.fasta -out GCF_002901905.1_ASM290190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:06,940] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:06,943] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:06,944] [INFO] Target genome list was writen to GCF_002901905.1_ASM290190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:06,955] [INFO] Task started: fastANI
[2024-01-24 13:41:06,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb33825-bcbd-48fb-9632-4a901ac8ab60/GCF_002901905.1_ASM290190v1_genomic.fna.gz --refList GCF_002901905.1_ASM290190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002901905.1_ASM290190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:15,363] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:15,376] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:15,376] [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_003019275.1	s__Staphylococcus muscae	99.9886	616	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	4	conclusive
GCF_000934465.1	s__Staphylococcus microti	81.9139	465	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.97	0.98	0.96	3	-
GCF_002902145.1	s__Staphylococcus rostri	81.7442	463	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013463155.1	s__Staphylococcus sp013463155	79.7879	332	616	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	78.9796	232	616	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	78.9392	238	616	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	78.8405	242	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900183575.1	s__Staphylococcus cornubiensis	78.8184	245	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901865.1	s__Staphylococcus agnetis	78.7842	211	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCF_000816085.1	s__Staphylococcus hyicus	78.5999	209	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
GCF_002902085.1	s__Staphylococcus simiae	77.5802	145	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
GCF_900097965.1	s__Staphylococcus caeli	77.5713	145	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003718735.1	s__Staphylococcus debuckii	77.5684	131	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902235.1	s__Staphylococcus ureilyticus	77.4698	128	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,378] [INFO] GTDB search result was written to GCF_002901905.1_ASM290190v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:15,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:15,382] [INFO] DFAST_QC result json was written to GCF_002901905.1_ASM290190v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:15,382] [INFO] DFAST_QC completed!
[2024-01-24 13:41:15,383] [INFO] Total running time: 0h0m45s