[2024-01-24 13:18:33,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg7161c8f2-8f37-4547-8b47-b4dde220a68f/dqc_reference
[2024-01-24 13:18:34,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,874] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg000f0a29-2dcf-478e-b017-54c474965578/GCF_014180735.1_ASM1418073v1_genomic.fna.gz | prodigal -d GCF_014180735.1_ASM1418073v1_genomic.fna/cds.fna -a GCF_014180735.1_ASM1418073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:39,744] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:39,744] [INFO] Task started: HMMsearch
[2024-01-24 13:18:39,744] [INFO] Running command: hmmsearch --tblout GCF_014180735.1_ASM1418073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7161c8f2-8f37-4547-8b47-b4dde220a68f/dqc_reference/reference_markers.hmm GCF_014180735.1_ASM1418073v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:40,067] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:40,068] [INFO] Found 6/6 markers.
[2024-01-24 13:18:40,091] [INFO] Query marker FASTA was written to GCF_014180735.1_ASM1418073v1_genomic.fna/markers.fasta
[2024-01-24 13:18:40,091] [INFO] Task started: Blastn
[2024-01-24 13:18:40,091] [INFO] Running command: blastn -query GCF_014180735.1_ASM1418073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7161c8f2-8f37-4547-8b47-b4dde220a68f/dqc_reference/reference_markers.fasta -out GCF_014180735.1_ASM1418073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:40,742] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:40,745] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:40,746] [INFO] Target genome list was writen to GCF_014180735.1_ASM1418073v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:40,762] [INFO] Task started: fastANI
[2024-01-24 13:18:40,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg000f0a29-2dcf-478e-b017-54c474965578/GCF_014180735.1_ASM1418073v1_genomic.fna.gz --refList GCF_014180735.1_ASM1418073v1_genomic.fna/target_genomes.txt --output GCF_014180735.1_ASM1418073v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:48,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:48,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7161c8f2-8f37-4547-8b47-b4dde220a68f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:48,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7161c8f2-8f37-4547-8b47-b4dde220a68f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:48,781] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:48,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:48,782] [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 cohnii subsp. barensis	strain=SC5	GCA_014180735.1	2834574	29382	type	True	100.0	862	863	95	conclusive
Staphylococcus cohnii subsp. cohnii	strain=NCTC 11041	GCA_002902365.1	74704	29382	suspected-type	True	95.8332	775	863	95	conclusive
Staphylococcus cohnii	strain=NCTC11041	GCA_900458255.1	29382	29382	type	True	95.7579	795	863	95	conclusive
Staphylococcus ureilyticus	strain=DSM 6718	GCA_002902235.1	94138	94138	type	True	91.8034	731	863	95	below_threshold
Staphylococcus nepalensis	strain=NCTC13834	GCA_900458695.1	214473	214473	type	True	83.4848	709	863	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	80.6058	518	863	95	below_threshold
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_001006765.1	224030	61015	type	True	80.3077	489	863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:48,784] [INFO] DFAST Taxonomy check result was written to GCF_014180735.1_ASM1418073v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:48,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:48,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:48,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7161c8f2-8f37-4547-8b47-b4dde220a68f/dqc_reference/checkm_data
[2024-01-24 13:18:48,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:48,840] [INFO] Task started: CheckM
[2024-01-24 13:18:48,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014180735.1_ASM1418073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014180735.1_ASM1418073v1_genomic.fna/checkm_input GCF_014180735.1_ASM1418073v1_genomic.fna/checkm_result
[2024-01-24 13:19:11,789] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:11,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:11,808] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:11,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:11,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014180735.1_ASM1418073v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:11,809] [INFO] Task started: Blastn
[2024-01-24 13:19:11,809] [INFO] Running command: blastn -query GCF_014180735.1_ASM1418073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7161c8f2-8f37-4547-8b47-b4dde220a68f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014180735.1_ASM1418073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:12,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:12,674] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:12,675] [INFO] Target genome list was writen to GCF_014180735.1_ASM1418073v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:12,695] [INFO] Task started: fastANI
[2024-01-24 13:19:12,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg000f0a29-2dcf-478e-b017-54c474965578/GCF_014180735.1_ASM1418073v1_genomic.fna.gz --refList GCF_014180735.1_ASM1418073v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014180735.1_ASM1418073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:22,326] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:22,338] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:22,339] [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_002902365.1	s__Staphylococcus cohnii	95.8332	775	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	conclusive
GCF_002902235.1	s__Staphylococcus ureilyticus	91.8346	729	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_014635045.1	s__Staphylococcus nepalensis	83.3963	716	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.49	99.27	0.96	0.93	23	-
GCF_000010125.1	s__Staphylococcus saprophyticus	80.6967	527	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_900458565.1	s__Staphylococcus equorum	80.6861	523	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_001747895.1	s__Staphylococcus equorum_A	80.6316	521	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	98.64	0.94	0.92	4	-
GCF_016774515.1	s__Staphylococcus xylosus_A	80.5039	519	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_001431205.1	s__Staphylococcus sp001431205	80.4999	498	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002732165.1	s__Staphylococcus xylosus	80.4371	510	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_001006765.1	s__Staphylococcus succinus	80.3077	489	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_002614725.1	s__Staphylococcus edaphicus	80.2376	480	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391405.1	s__Staphylococcus sp013391405	80.1539	504	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900097965.1	s__Staphylococcus caeli	80.0688	471	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000875895.1	s__Staphylococcus gallinarum	79.7433	444	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.63	98.14	0.94	0.91	25	-
GCF_003491325.1	s__Staphylococcus warneri_A	78.4362	276	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:22,341] [INFO] GTDB search result was written to GCF_014180735.1_ASM1418073v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:22,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:22,344] [INFO] DFAST_QC result json was written to GCF_014180735.1_ASM1418073v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:22,345] [INFO] DFAST_QC completed!
[2024-01-24 13:19:22,345] [INFO] Total running time: 0h0m49s