[2024-01-24 14:30:34,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,140] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e6070d0-a97d-498b-a63c-b628a96de5e4/dqc_reference
[2024-01-24 14:30:35,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:35,638] [INFO] Task started: Prodigal
[2024-01-24 14:30:35,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg769dee58-7f2e-49c8-abbb-ee815e8213d4/GCF_006539925.1_ASM653992v1_genomic.fna.gz | prodigal -d GCF_006539925.1_ASM653992v1_genomic.fna/cds.fna -a GCF_006539925.1_ASM653992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:48,494] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:48,495] [INFO] Task started: HMMsearch
[2024-01-24 14:30:48,495] [INFO] Running command: hmmsearch --tblout GCF_006539925.1_ASM653992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e6070d0-a97d-498b-a63c-b628a96de5e4/dqc_reference/reference_markers.hmm GCF_006539925.1_ASM653992v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:48,848] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:48,849] [INFO] Found 6/6 markers.
[2024-01-24 14:30:48,884] [INFO] Query marker FASTA was written to GCF_006539925.1_ASM653992v1_genomic.fna/markers.fasta
[2024-01-24 14:30:48,885] [INFO] Task started: Blastn
[2024-01-24 14:30:48,885] [INFO] Running command: blastn -query GCF_006539925.1_ASM653992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e6070d0-a97d-498b-a63c-b628a96de5e4/dqc_reference/reference_markers.fasta -out GCF_006539925.1_ASM653992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:49,903] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:49,912] [INFO] Selected 14 target genomes.
[2024-01-24 14:30:49,912] [INFO] Target genome list was writen to GCF_006539925.1_ASM653992v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:49,918] [INFO] Task started: fastANI
[2024-01-24 14:30:49,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg769dee58-7f2e-49c8-abbb-ee815e8213d4/GCF_006539925.1_ASM653992v1_genomic.fna.gz --refList GCF_006539925.1_ASM653992v1_genomic.fna/target_genomes.txt --output GCF_006539925.1_ASM653992v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:00,886] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:00,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e6070d0-a97d-498b-a63c-b628a96de5e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:00,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e6070d0-a97d-498b-a63c-b628a96de5e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:00,903] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:00,903] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:00,903] [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 uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	100.0	1238	1240	95	conclusive
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	83.6578	733	1240	95	below_threshold
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	83.6253	748	1240	95	below_threshold
Glutamicibacter nicotianae	strain=NBRC 14234	GCA_006539525.1	37929	37929	type	True	82.2737	633	1240	95	below_threshold
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	82.2699	636	1240	95	below_threshold
Glutamicibacter mysorens	strain=DSM 12798	GCA_002797775.1	257984	257984	type	True	82.2455	628	1240	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	81.3557	589	1240	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	79.5744	470	1240	95	below_threshold
Arthrobacter ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	78.1054	232	1240	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.9526	213	1240	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.9424	212	1240	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.2632	205	1240	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	77.1507	116	1240	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.6559	123	1240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:00,905] [INFO] DFAST Taxonomy check result was written to GCF_006539925.1_ASM653992v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:00,905] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:00,905] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:00,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e6070d0-a97d-498b-a63c-b628a96de5e4/dqc_reference/checkm_data
[2024-01-24 14:31:00,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:00,953] [INFO] Task started: CheckM
[2024-01-24 14:31:00,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539925.1_ASM653992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539925.1_ASM653992v1_genomic.fna/checkm_input GCF_006539925.1_ASM653992v1_genomic.fna/checkm_result
[2024-01-24 14:31:39,651] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:39,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:39,677] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:39,677] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:39,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539925.1_ASM653992v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:39,678] [INFO] Task started: Blastn
[2024-01-24 14:31:39,679] [INFO] Running command: blastn -query GCF_006539925.1_ASM653992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e6070d0-a97d-498b-a63c-b628a96de5e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539925.1_ASM653992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:41,327] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:41,330] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:41,331] [INFO] Target genome list was writen to GCF_006539925.1_ASM653992v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:41,343] [INFO] Task started: fastANI
[2024-01-24 14:31:41,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg769dee58-7f2e-49c8-abbb-ee815e8213d4/GCF_006539925.1_ASM653992v1_genomic.fna.gz --refList GCF_006539925.1_ASM653992v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539925.1_ASM653992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:51,707] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:51,724] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:51,724] [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_006539925.1	s__Glutamicibacter uratoxydans	100.0	1238	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003309065.1	s__Glutamicibacter soli	83.7427	766	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.33	97.69	0.91	0.87	6	-
GCF_014647495.1	s__Glutamicibacter protophormiae	83.6828	731	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.76	97.53	0.93	0.87	3	-
GCF_006539525.1	s__Glutamicibacter nicotianae	82.2898	631	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	97.59	96.22	0.88	0.85	10	-
GCF_002979865.1	s__Glutamicibacter sp002979865	81.573	623	1240	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	81.3443	590	1240	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	80.7025	545	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.17	97.78	0.92	0.89	4	-
GCF_900094805.1	s__Glutamicibacter sp900094805	80.478	433	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003287975.1	s__Paeniglutamicibacter sp003287975	79.6945	447	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876575.1	s__Paeniglutamicibacter psychrophenolicus	79.6007	468	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900010755.1	s__Paeniglutamicibacter antarcticus_A	79.1889	379	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348945.1	s__Paeniglutamicibacter gangotriensis	78.7783	372	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	97.63	97.63	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:51,726] [INFO] GTDB search result was written to GCF_006539925.1_ASM653992v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:51,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:51,731] [INFO] DFAST_QC result json was written to GCF_006539925.1_ASM653992v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:51,731] [INFO] DFAST_QC completed!
[2024-01-24 14:31:51,731] [INFO] Total running time: 0h1m18s