[2024-01-25 20:13:20,466] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:20,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:20,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bb9ed00-60ff-4724-978a-ab52ba8f77b1/dqc_reference
[2024-01-25 20:13:21,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:21,620] [INFO] Task started: Prodigal
[2024-01-25 20:13:21,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg16c74acc-5589-4298-aa47-e962bc260ec1/GCF_002902085.1_ASM290208v1_genomic.fna.gz | prodigal -d GCF_002902085.1_ASM290208v1_genomic.fna/cds.fna -a GCF_002902085.1_ASM290208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:25,406] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:25,407] [INFO] Task started: HMMsearch
[2024-01-25 20:13:25,407] [INFO] Running command: hmmsearch --tblout GCF_002902085.1_ASM290208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bb9ed00-60ff-4724-978a-ab52ba8f77b1/dqc_reference/reference_markers.hmm GCF_002902085.1_ASM290208v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:25,613] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:25,614] [INFO] Found 6/6 markers.
[2024-01-25 20:13:25,636] [INFO] Query marker FASTA was written to GCF_002902085.1_ASM290208v1_genomic.fna/markers.fasta
[2024-01-25 20:13:25,637] [INFO] Task started: Blastn
[2024-01-25 20:13:25,637] [INFO] Running command: blastn -query GCF_002902085.1_ASM290208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bb9ed00-60ff-4724-978a-ab52ba8f77b1/dqc_reference/reference_markers.fasta -out GCF_002902085.1_ASM290208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:26,222] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:26,226] [INFO] Selected 16 target genomes.
[2024-01-25 20:13:26,226] [INFO] Target genome list was writen to GCF_002902085.1_ASM290208v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:26,285] [INFO] Task started: fastANI
[2024-01-25 20:13:26,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c74acc-5589-4298-aa47-e962bc260ec1/GCF_002902085.1_ASM290208v1_genomic.fna.gz --refList GCF_002902085.1_ASM290208v1_genomic.fna/target_genomes.txt --output GCF_002902085.1_ASM290208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:35,654] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:35,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bb9ed00-60ff-4724-978a-ab52ba8f77b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:35,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bb9ed00-60ff-4724-978a-ab52ba8f77b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:35,664] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:13:35,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:35,664] [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 simiae	strain=CCUG 51256	GCA_002902085.1	308354	308354	type	True	100.0	812	815	95	conclusive
Staphylococcus simiae	strain=NCTC13838	GCA_900187055.1	308354	308354	type	True	99.9884	812	815	95	conclusive
Staphylococcus simiae	strain=CCM 7213	GCA_000235645.2	308354	308354	type	True	99.8004	702	815	95	conclusive
Staphylococcus argenteus	strain=MSHR1132	GCA_000236925.1	985002	985002	type	True	80.9603	487	815	95	below_threshold
Staphylococcus argenteus	strain=DSM 28299	GCA_014877305.1	985002	985002	type	True	80.9235	490	815	95	below_threshold
Staphylococcus schweitzeri	strain=DSM 28300	GCA_014877095.1	1654388	1654388	type	True	80.8465	486	815	95	below_threshold
Staphylococcus schweitzeri	strain=NCTC13712	GCA_900636685.1	1654388	1654388	type	True	80.8233	490	815	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	80.7391	498	815	95	below_threshold
Staphylococcus aureus	strain=DSM 20231	GCA_001027105.1	1280	1280	type	True	80.6749	499	815	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	80.613	505	815	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.3501	314	815	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	79.1949	309	815	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	79.1583	300	815	95	below_threshold
Staphylococcus devriesei	strain=CCUG 58238	GCA_002902625.1	586733	586733	type	True	78.9157	302	815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:35,667] [INFO] DFAST Taxonomy check result was written to GCF_002902085.1_ASM290208v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:35,669] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:35,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:35,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bb9ed00-60ff-4724-978a-ab52ba8f77b1/dqc_reference/checkm_data
[2024-01-25 20:13:35,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:35,700] [INFO] Task started: CheckM
[2024-01-25 20:13:35,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902085.1_ASM290208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902085.1_ASM290208v1_genomic.fna/checkm_input GCF_002902085.1_ASM290208v1_genomic.fna/checkm_result
[2024-01-25 20:13:53,494] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:53,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:53,511] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:53,512] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:53,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902085.1_ASM290208v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:53,512] [INFO] Task started: Blastn
[2024-01-25 20:13:53,512] [INFO] Running command: blastn -query GCF_002902085.1_ASM290208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bb9ed00-60ff-4724-978a-ab52ba8f77b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902085.1_ASM290208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:54,253] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:54,256] [INFO] Selected 11 target genomes.
[2024-01-25 20:13:54,256] [INFO] Target genome list was writen to GCF_002902085.1_ASM290208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:54,263] [INFO] Task started: fastANI
[2024-01-25 20:13:54,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c74acc-5589-4298-aa47-e962bc260ec1/GCF_002902085.1_ASM290208v1_genomic.fna.gz --refList GCF_002902085.1_ASM290208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902085.1_ASM290208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:01,212] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:01,220] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:01,220] [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_002902085.1	s__Staphylococcus simiae	100.0	812	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	conclusive
GCF_017357005.1	s__Staphylococcus simiae_A	94.4615	746	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.91	0.98	0.98	6	-
GCF_000236925.1	s__Staphylococcus argenteus	80.9511	488	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.00	98.60	0.96	0.90	171	-
GCF_015025035.1	s__Staphylococcus sp015025035	80.9152	491	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
GCF_002902405.1	s__Staphylococcus schweitzeri	80.8778	482	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	-
GCF_001027105.1	s__Staphylococcus aureus	80.6866	498	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.78	97.08	0.95	0.88	13059	-
GCF_003491325.1	s__Staphylococcus warneri_A	79.5133	369	815	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	79.1583	300	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_006094395.1	s__Staphylococcus haemolyticus	78.9281	324	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_002902625.1	s__Staphylococcus devriesei	78.9157	302	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
GCF_013391405.1	s__Staphylococcus sp013391405	78.5151	260	815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:01,221] [INFO] GTDB search result was written to GCF_002902085.1_ASM290208v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:01,222] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:01,225] [INFO] DFAST_QC result json was written to GCF_002902085.1_ASM290208v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:01,226] [INFO] DFAST_QC completed!
[2024-01-25 20:14:01,226] [INFO] Total running time: 0h0m41s