[2024-01-25 19:01:50,588] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:50,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:50,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg6448b5c6-97c1-42d0-9e49-6ec5287a1b82/dqc_reference
[2024-01-25 19:01:51,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:51,761] [INFO] Task started: Prodigal
[2024-01-25 19:01:51,761] [INFO] Running command: gunzip -c /var/lib/cwl/stg0464a289-d870-4b3f-8480-ea5117e2c6c8/GCF_900458705.1_50432_E01_genomic.fna.gz | prodigal -d GCF_900458705.1_50432_E01_genomic.fna/cds.fna -a GCF_900458705.1_50432_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:56,735] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:56,735] [INFO] Task started: HMMsearch
[2024-01-25 19:01:56,735] [INFO] Running command: hmmsearch --tblout GCF_900458705.1_50432_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6448b5c6-97c1-42d0-9e49-6ec5287a1b82/dqc_reference/reference_markers.hmm GCF_900458705.1_50432_E01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:56,968] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:56,970] [INFO] Found 6/6 markers.
[2024-01-25 19:01:56,992] [INFO] Query marker FASTA was written to GCF_900458705.1_50432_E01_genomic.fna/markers.fasta
[2024-01-25 19:01:56,993] [INFO] Task started: Blastn
[2024-01-25 19:01:56,993] [INFO] Running command: blastn -query GCF_900458705.1_50432_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6448b5c6-97c1-42d0-9e49-6ec5287a1b82/dqc_reference/reference_markers.fasta -out GCF_900458705.1_50432_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:57,563] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:57,567] [INFO] Selected 10 target genomes.
[2024-01-25 19:01:57,568] [INFO] Target genome list was writen to GCF_900458705.1_50432_E01_genomic.fna/target_genomes.txt
[2024-01-25 19:01:57,572] [INFO] Task started: fastANI
[2024-01-25 19:01:57,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg0464a289-d870-4b3f-8480-ea5117e2c6c8/GCF_900458705.1_50432_E01_genomic.fna.gz --refList GCF_900458705.1_50432_E01_genomic.fna/target_genomes.txt --output GCF_900458705.1_50432_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:03,953] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:03,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6448b5c6-97c1-42d0-9e49-6ec5287a1b82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:03,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6448b5c6-97c1-42d0-9e49-6ec5287a1b82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:03,960] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:02:03,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:03,960] [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 microti	strain=NCTC13832	GCA_900458705.1	569857	569857	type	True	100.0	819	826	95	conclusive
Staphylococcus microti	strain=DSM 22147	GCA_000934465.1	569857	569857	type	True	99.9317	745	826	95	conclusive
Staphylococcus microti	strain=DSM 22147	GCA_002902635.1	569857	569857	type	True	99.8875	719	826	95	conclusive
Staphylococcus rostri	strain=DSM 21968	GCA_002902145.1	522262	522262	type	True	84.6344	579	826	95	below_threshold
Staphylococcus muscae	strain=NCTC13833	GCA_900187005.1	1294	1294	type	True	82.0731	512	826	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	79.3841	51	826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:03,961] [INFO] DFAST Taxonomy check result was written to GCF_900458705.1_50432_E01_genomic.fna/tc_result.tsv
[2024-01-25 19:02:03,961] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:03,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:03,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6448b5c6-97c1-42d0-9e49-6ec5287a1b82/dqc_reference/checkm_data
[2024-01-25 19:02:03,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:03,990] [INFO] Task started: CheckM
[2024-01-25 19:02:03,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900458705.1_50432_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900458705.1_50432_E01_genomic.fna/checkm_input GCF_900458705.1_50432_E01_genomic.fna/checkm_result
[2024-01-25 19:02:24,535] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:24,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:24,550] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:24,550] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:24,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900458705.1_50432_E01_genomic.fna/markers.fasta)
[2024-01-25 19:02:24,551] [INFO] Task started: Blastn
[2024-01-25 19:02:24,551] [INFO] Running command: blastn -query GCF_900458705.1_50432_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6448b5c6-97c1-42d0-9e49-6ec5287a1b82/dqc_reference/reference_markers_gtdb.fasta -out GCF_900458705.1_50432_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:25,309] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:25,312] [INFO] Selected 16 target genomes.
[2024-01-25 19:02:25,312] [INFO] Target genome list was writen to GCF_900458705.1_50432_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:25,343] [INFO] Task started: fastANI
[2024-01-25 19:02:25,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg0464a289-d870-4b3f-8480-ea5117e2c6c8/GCF_900458705.1_50432_E01_genomic.fna.gz --refList GCF_900458705.1_50432_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900458705.1_50432_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:33,526] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:33,537] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:33,538] [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_000934465.1	s__Staphylococcus microti	99.9317	745	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.97	0.98	0.96	3	conclusive
GCF_002902145.1	s__Staphylococcus rostri	84.6434	578	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003019275.1	s__Staphylococcus muscae	81.9779	514	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	4	-
GCF_013463155.1	s__Staphylococcus sp013463155	80.5942	388	826	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	80.1186	294	826	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	79.6816	312	826	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	79.4528	273	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	79.3557	264	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_002101335.1	s__Staphylococcus lutrae	79.228	231	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900183575.1	s__Staphylococcus cornubiensis	79.2204	314	826	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	79.1778	293	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_002901945.1	s__Staphylococcus chromogenes	78.7452	222	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.79	96.35	0.95	0.90	130	-
GCF_004117835.1	s__Macrococcus_B sp004117835	78.4624	107	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002902575.1	s__Staphylococcus croceilyticus	78.2903	178	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002902565.1	s__Staphylococcus petrasii	78.1255	161	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:33,539] [INFO] GTDB search result was written to GCF_900458705.1_50432_E01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:33,540] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:33,546] [INFO] DFAST_QC result json was written to GCF_900458705.1_50432_E01_genomic.fna/dqc_result.json
[2024-01-25 19:02:33,547] [INFO] DFAST_QC completed!
[2024-01-25 19:02:33,547] [INFO] Total running time: 0h0m43s