[2024-01-24 14:28:03,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:03,103] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:03,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg62984dd6-5a77-42d2-be5a-1e1ff422dba9/dqc_reference
[2024-01-24 14:28:04,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,349] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,349] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ea72a13-3e66-46cc-8624-c6c6bb7fbe46/GCF_002902165.1_ASM290216v1_genomic.fna.gz | prodigal -d GCF_002902165.1_ASM290216v1_genomic.fna/cds.fna -a GCF_002902165.1_ASM290216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:09,441] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:09,442] [INFO] Task started: HMMsearch
[2024-01-24 14:28:09,442] [INFO] Running command: hmmsearch --tblout GCF_002902165.1_ASM290216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62984dd6-5a77-42d2-be5a-1e1ff422dba9/dqc_reference/reference_markers.hmm GCF_002902165.1_ASM290216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:09,707] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:09,709] [INFO] Found 6/6 markers.
[2024-01-24 14:28:09,735] [INFO] Query marker FASTA was written to GCF_002902165.1_ASM290216v1_genomic.fna/markers.fasta
[2024-01-24 14:28:09,735] [INFO] Task started: Blastn
[2024-01-24 14:28:09,735] [INFO] Running command: blastn -query GCF_002902165.1_ASM290216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62984dd6-5a77-42d2-be5a-1e1ff422dba9/dqc_reference/reference_markers.fasta -out GCF_002902165.1_ASM290216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:10,327] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:10,331] [INFO] Selected 19 target genomes.
[2024-01-24 14:28:10,332] [INFO] Target genome list was writen to GCF_002902165.1_ASM290216v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:10,352] [INFO] Task started: fastANI
[2024-01-24 14:28:10,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea72a13-3e66-46cc-8624-c6c6bb7fbe46/GCF_002902165.1_ASM290216v1_genomic.fna.gz --refList GCF_002902165.1_ASM290216v1_genomic.fna/target_genomes.txt --output GCF_002902165.1_ASM290216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:20,902] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:20,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62984dd6-5a77-42d2-be5a-1e1ff422dba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:20,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62984dd6-5a77-42d2-be5a-1e1ff422dba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:20,916] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:20,916] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:20,916] [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 lutrae	strain=DSM 10244	GCA_002902165.1	155085	155085	type	True	100.0	734	742	95	conclusive
Staphylococcus lutrae	strain=ATCC 700373	GCA_002101335.1	155085	155085	type	True	99.9859	740	742	95	conclusive
Staphylococcus delphini	strain=NCTC12225	GCA_900636325.1	53344	53344	type	True	81.0091	481	742	95	below_threshold
Staphylococcus delphini	strain=NCTC 12225	GCA_002902785.1	53344	53344	type	True	80.9839	463	742	95	below_threshold
Staphylococcus delphini	strain=Heidy	GCA_003585325.1	53344	53344	type	True	80.9366	483	742	95	below_threshold
Staphylococcus pseudintermedius	strain=CCUG 49543	GCA_002902125.1	283734	283734	type	True	80.8503	439	742	95	below_threshold
Staphylococcus pseudintermedius	strain=FDAARGOS_930	GCA_016026635.1	283734	283734	type	True	80.8274	457	742	95	below_threshold
Staphylococcus cornubiensis	strain=NW1	GCA_900183575.1	1986155	1986155	type	True	80.8093	469	742	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_002902385.1	1285	1285	type	True	80.7489	430	742	95	below_threshold
Staphylococcus pseudintermedius	strain=LMG 22219	GCA_001792775.2	283734	283734	type	True	80.741	467	742	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	80.6748	417	742	95	below_threshold
Staphylococcus coagulans	strain=DSM 6628	GCA_002901995.1	74706	74706	type	True	79.4508	337	742	95	below_threshold
Staphylococcus schleiferi	strain=ATCC 43808	GCA_011137195.1	1295	1295	type	True	79.3812	340	742	95	below_threshold
Staphylococcus schleiferi subsp. schleiferi	strain=NCTC 12218	GCA_003968865.1	74707	1295	type	True	79.3122	336	742	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	77.8617	130	742	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	77.7955	132	742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:20,918] [INFO] DFAST Taxonomy check result was written to GCF_002902165.1_ASM290216v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:20,919] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:20,919] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:20,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62984dd6-5a77-42d2-be5a-1e1ff422dba9/dqc_reference/checkm_data
[2024-01-24 14:28:20,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:20,966] [INFO] Task started: CheckM
[2024-01-24 14:28:20,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902165.1_ASM290216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902165.1_ASM290216v1_genomic.fna/checkm_input GCF_002902165.1_ASM290216v1_genomic.fna/checkm_result
[2024-01-24 14:28:44,470] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:44,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:44,491] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:44,492] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:44,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902165.1_ASM290216v1_genomic.fna/markers.fasta)
[2024-01-24 14:28:44,493] [INFO] Task started: Blastn
[2024-01-24 14:28:44,493] [INFO] Running command: blastn -query GCF_002902165.1_ASM290216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62984dd6-5a77-42d2-be5a-1e1ff422dba9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902165.1_ASM290216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:45,354] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:45,357] [INFO] Selected 13 target genomes.
[2024-01-24 14:28:45,357] [INFO] Target genome list was writen to GCF_002902165.1_ASM290216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:45,379] [INFO] Task started: fastANI
[2024-01-24 14:28:45,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea72a13-3e66-46cc-8624-c6c6bb7fbe46/GCF_002902165.1_ASM290216v1_genomic.fna.gz --refList GCF_002902165.1_ASM290216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902165.1_ASM290216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:28:52,691] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:52,704] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:28:52,705] [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_002101335.1	s__Staphylococcus lutrae	99.9859	740	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900636325.1	s__Staphylococcus delphini	81.0082	482	742	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	80.9415	458	742	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	80.8093	469	742	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	80.7401	430	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	80.7325	468	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_002901995.1	s__Staphylococcus coagulans	79.4508	337	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCA_900458895.2	s__Staphylococcus schleiferi	79.4023	335	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_003012915.1	s__Staphylococcus felis	78.7073	210	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.05	98.64	0.95	0.91	31	-
GCF_013463155.1	s__Staphylococcus sp013463155	78.701	213	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000816085.1	s__Staphylococcus hyicus	78.4595	211	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
GCF_002901865.1	s__Staphylococcus agnetis	78.3737	231	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCF_016774515.1	s__Staphylococcus xylosus_A	77.8324	115	742	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:28:52,707] [INFO] GTDB search result was written to GCF_002902165.1_ASM290216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:28:52,707] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:28:52,711] [INFO] DFAST_QC result json was written to GCF_002902165.1_ASM290216v1_genomic.fna/dqc_result.json
[2024-01-24 14:28:52,711] [INFO] DFAST_QC completed!
[2024-01-24 14:28:52,711] [INFO] Total running time: 0h0m50s