[2024-01-25 20:21:35,661] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgcca356c3-d34b-47f8-998f-686fe9e01cb6/dqc_reference
[2024-01-25 20:21:36,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,835] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,835] [INFO] Running command: gunzip -c /var/lib/cwl/stg042991b0-56bc-4a6c-8866-13143d00ee7f/GCF_003259675.1_ASM325967v1_genomic.fna.gz | prodigal -d GCF_003259675.1_ASM325967v1_genomic.fna/cds.fna -a GCF_003259675.1_ASM325967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:40,824] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:40,825] [INFO] Task started: HMMsearch
[2024-01-25 20:21:40,825] [INFO] Running command: hmmsearch --tblout GCF_003259675.1_ASM325967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcca356c3-d34b-47f8-998f-686fe9e01cb6/dqc_reference/reference_markers.hmm GCF_003259675.1_ASM325967v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:41,044] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:41,045] [INFO] Found 6/6 markers.
[2024-01-25 20:21:41,068] [INFO] Query marker FASTA was written to GCF_003259675.1_ASM325967v1_genomic.fna/markers.fasta
[2024-01-25 20:21:41,068] [INFO] Task started: Blastn
[2024-01-25 20:21:41,068] [INFO] Running command: blastn -query GCF_003259675.1_ASM325967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcca356c3-d34b-47f8-998f-686fe9e01cb6/dqc_reference/reference_markers.fasta -out GCF_003259675.1_ASM325967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:41,637] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:41,640] [INFO] Selected 16 target genomes.
[2024-01-25 20:21:41,640] [INFO] Target genome list was writen to GCF_003259675.1_ASM325967v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:41,656] [INFO] Task started: fastANI
[2024-01-25 20:21:41,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg042991b0-56bc-4a6c-8866-13143d00ee7f/GCF_003259675.1_ASM325967v1_genomic.fna.gz --refList GCF_003259675.1_ASM325967v1_genomic.fna/target_genomes.txt --output GCF_003259675.1_ASM325967v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:49,143] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:49,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcca356c3-d34b-47f8-998f-686fe9e01cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:49,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcca356c3-d34b-47f8-998f-686fe9e01cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:49,151] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:49,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:49,151] [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
Macrococcus bohemicus	strain=03/115	GCA_003259675.1	1903056	1903056	type	True	100.0	791	791	95	conclusive
Macrococcus epidermidis	strain=01/688	GCA_003259695.1	1902580	1902580	type	True	93.5314	672	791	95	below_threshold
Macrococcus goetzii	strain=CCM 4927	GCA_002742385.2	1891097	1891097	type	True	92.9525	667	791	95	below_threshold
Macrococcus caseolyticus subsp. hominis	strain=CCM 7927	GCA_002742395.2	1891096	69966	type	True	82.1614	284	791	95	below_threshold
Macrococcus caseolyticus	strain=FDAARGOS_868	GCA_016028795.1	69966	69966	type	True	81.615	299	791	95	below_threshold
Macrococcus canis	strain=KM 45013	GCA_002119805.1	1855823	1855823	type	True	81.0229	277	791	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	80.2865	289	791	95	below_threshold
Mammaliicoccus fleurettii	strain=NCTC13829	GCA_900458505.1	150056	150056	type	True	78.359	127	791	95	below_threshold
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	78.2128	135	791	95	below_threshold
Staphylococcus caprae	strain=NCTC12196	GCA_900458385.1	29380	29380	type	True	77.6284	96	791	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:49,154] [INFO] DFAST Taxonomy check result was written to GCF_003259675.1_ASM325967v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:49,155] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:49,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:49,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcca356c3-d34b-47f8-998f-686fe9e01cb6/dqc_reference/checkm_data
[2024-01-25 20:21:49,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:49,181] [INFO] Task started: CheckM
[2024-01-25 20:21:49,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259675.1_ASM325967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259675.1_ASM325967v1_genomic.fna/checkm_input GCF_003259675.1_ASM325967v1_genomic.fna/checkm_result
[2024-01-25 20:22:07,463] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:07,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:07,482] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:07,483] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:07,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259675.1_ASM325967v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:07,483] [INFO] Task started: Blastn
[2024-01-25 20:22:07,483] [INFO] Running command: blastn -query GCF_003259675.1_ASM325967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcca356c3-d34b-47f8-998f-686fe9e01cb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259675.1_ASM325967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:08,241] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:08,244] [INFO] Selected 14 target genomes.
[2024-01-25 20:22:08,244] [INFO] Target genome list was writen to GCF_003259675.1_ASM325967v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:08,259] [INFO] Task started: fastANI
[2024-01-25 20:22:08,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg042991b0-56bc-4a6c-8866-13143d00ee7f/GCF_003259675.1_ASM325967v1_genomic.fna.gz --refList GCF_003259675.1_ASM325967v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259675.1_ASM325967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:16,407] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:16,417] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:16,417] [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_003259675.1	s__Macrococcus_B bohemicus	100.0	791	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	98.03	97.95	0.86	0.85	5	conclusive
GCF_003259695.1	s__Macrococcus_B epidermidis	93.5314	672	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	N/A	N/A	N/A	N/A	1	-
GCF_002742385.2	s__Macrococcus_B goetzii	92.9525	667	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	96.60	96.57	0.86	0.86	4	-
GCF_002902665.1	s__Macrococcus_B caseolyticus	81.6025	289	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	98.20	96.60	0.90	0.84	54	-
GCF_002119805.1	s__Macrococcus_B canis	81.0229	277	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	96.44	96.14	0.86	0.82	14	-
GCF_004117835.1	s__Macrococcus_B sp004117835	79.2453	272	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359545.1	s__Macrococcus lamae	78.3559	123	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901825.1	s__Mammaliicoccus sciuri	78.1749	137	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
GCF_003970575.1	s__Mammaliicoccus fleurettii	78.1229	128	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.35	98.97	0.91	0.88	9	-
GCF_000816085.1	s__Staphylococcus hyicus	77.9592	84	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
GCF_002901845.1	s__Staphylococcus hominis	77.7324	86	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
GCF_002902725.1	s__Staphylococcus caprae	77.5099	94	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_001455345.1	s__Bacillus_A thuringiensis_N	76.6289	50	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.23	95.30	0.91	0.84	24	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:16,419] [INFO] GTDB search result was written to GCF_003259675.1_ASM325967v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:16,419] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:16,422] [INFO] DFAST_QC result json was written to GCF_003259675.1_ASM325967v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:16,422] [INFO] DFAST_QC completed!
[2024-01-25 20:22:16,423] [INFO] Total running time: 0h0m41s