[2024-01-24 15:10:22,256] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,258] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,258] [INFO] DQC Reference Directory: /var/lib/cwl/stg713725ec-bf0a-48ac-bdf4-efb45035c5cc/dqc_reference
[2024-01-24 15:10:23,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:23,854] [INFO] Task started: Prodigal
[2024-01-24 15:10:23,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgb25239fb-83bd-4be9-8fa2-fb5eb6185b05/GCF_017876615.1_ASM1787661v1_genomic.fna.gz | prodigal -d GCF_017876615.1_ASM1787661v1_genomic.fna/cds.fna -a GCF_017876615.1_ASM1787661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:35,800] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:35,800] [INFO] Task started: HMMsearch
[2024-01-24 15:10:35,800] [INFO] Running command: hmmsearch --tblout GCF_017876615.1_ASM1787661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg713725ec-bf0a-48ac-bdf4-efb45035c5cc/dqc_reference/reference_markers.hmm GCF_017876615.1_ASM1787661v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:36,064] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:36,065] [INFO] Found 6/6 markers.
[2024-01-24 15:10:36,102] [INFO] Query marker FASTA was written to GCF_017876615.1_ASM1787661v1_genomic.fna/markers.fasta
[2024-01-24 15:10:36,102] [INFO] Task started: Blastn
[2024-01-24 15:10:36,102] [INFO] Running command: blastn -query GCF_017876615.1_ASM1787661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg713725ec-bf0a-48ac-bdf4-efb45035c5cc/dqc_reference/reference_markers.fasta -out GCF_017876615.1_ASM1787661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:37,269] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:37,276] [INFO] Selected 12 target genomes.
[2024-01-24 15:10:37,276] [INFO] Target genome list was writen to GCF_017876615.1_ASM1787661v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:37,281] [INFO] Task started: fastANI
[2024-01-24 15:10:37,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgb25239fb-83bd-4be9-8fa2-fb5eb6185b05/GCF_017876615.1_ASM1787661v1_genomic.fna.gz --refList GCF_017876615.1_ASM1787661v1_genomic.fna/target_genomes.txt --output GCF_017876615.1_ASM1787661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:45,857] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:45,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg713725ec-bf0a-48ac-bdf4-efb45035c5cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:45,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg713725ec-bf0a-48ac-bdf4-efb45035c5cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:45,868] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:10:45,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:45,868] [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
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	100.0	1290	1290	95	conclusive
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	99.9717	1259	1290	95	conclusive
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	83.4368	755	1290	95	below_threshold
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	83.0127	742	1290	95	below_threshold
Glutamicibacter mysorens	strain=DSM 12798	GCA_002797775.1	257984	257984	type	True	82.9524	752	1290	95	below_threshold
Glutamicibacter nicotianae	strain=NBRC 14234	GCA_006539525.1	37929	37929	type	True	82.8263	718	1290	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	81.7538	604	1290	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.3845	305	1290	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.1783	299	1290	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.0737	175	1290	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	76.8504	139	1290	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	76.8357	148	1290	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:45,870] [INFO] DFAST Taxonomy check result was written to GCF_017876615.1_ASM1787661v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:45,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:45,871] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:45,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg713725ec-bf0a-48ac-bdf4-efb45035c5cc/dqc_reference/checkm_data
[2024-01-24 15:10:45,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:45,910] [INFO] Task started: CheckM
[2024-01-24 15:10:45,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876615.1_ASM1787661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876615.1_ASM1787661v1_genomic.fna/checkm_input GCF_017876615.1_ASM1787661v1_genomic.fna/checkm_result
[2024-01-24 15:11:22,854] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:22,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:22,873] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:22,873] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:22,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876615.1_ASM1787661v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:22,874] [INFO] Task started: Blastn
[2024-01-24 15:11:22,874] [INFO] Running command: blastn -query GCF_017876615.1_ASM1787661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg713725ec-bf0a-48ac-bdf4-efb45035c5cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876615.1_ASM1787661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:24,785] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:24,798] [INFO] Selected 9 target genomes.
[2024-01-24 15:11:24,799] [INFO] Target genome list was writen to GCF_017876615.1_ASM1787661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:24,808] [INFO] Task started: fastANI
[2024-01-24 15:11:24,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgb25239fb-83bd-4be9-8fa2-fb5eb6185b05/GCF_017876615.1_ASM1787661v1_genomic.fna.gz --refList GCF_017876615.1_ASM1787661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876615.1_ASM1787661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:34,015] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:34,024] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:34,024] [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_014647495.1	s__Glutamicibacter protophormiae	99.9717	1259	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.76	97.53	0.93	0.87	3	conclusive
GCF_003309065.1	s__Glutamicibacter soli	91.3865	1066	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.33	97.69	0.91	0.87	6	-
GCF_006539925.1	s__Glutamicibacter uratoxydans	83.4483	754	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539525.1	s__Glutamicibacter nicotianae	82.8406	716	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	97.59	96.22	0.88	0.85	10	-
GCF_000197735.1	s__Glutamicibacter arilaitensis	82.0302	682	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.79	97.54	0.91	0.83	7	-
GCF_002979865.1	s__Glutamicibacter sp002979865	81.9919	686	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.88	98.56	0.94	0.92	3	-
GCF_001302565.1	s__Glutamicibacter halophytocola	81.7198	603	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.28	98.01	0.91	0.89	4	-
GCF_006094275.1	s__Glutamicibacter creatinolyticus	81.6733	638	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.17	97.78	0.92	0.89	4	-
GCF_002975405.1	s__Glutamicibacter sp002975405	81.4183	587	1290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.44	96.03	0.93	0.84	6	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:34,031] [INFO] GTDB search result was written to GCF_017876615.1_ASM1787661v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:34,032] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:34,036] [INFO] DFAST_QC result json was written to GCF_017876615.1_ASM1787661v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:34,036] [INFO] DFAST_QC completed!
[2024-01-24 15:11:34,036] [INFO] Total running time: 0h1m12s