[2024-01-24 11:59:22,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg00022a97-e1d2-4254-914b-c3fb41c8cfaf/dqc_reference
[2024-01-24 11:59:25,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,643] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,644] [INFO] Running command: gunzip -c /var/lib/cwl/stgb848b600-7e42-4c61-8ca1-d06030f2f244/GCF_014647495.1_ASM1464749v1_genomic.fna.gz | prodigal -d GCF_014647495.1_ASM1464749v1_genomic.fna/cds.fna -a GCF_014647495.1_ASM1464749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:37,245] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:37,245] [INFO] Task started: HMMsearch
[2024-01-24 11:59:37,245] [INFO] Running command: hmmsearch --tblout GCF_014647495.1_ASM1464749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00022a97-e1d2-4254-914b-c3fb41c8cfaf/dqc_reference/reference_markers.hmm GCF_014647495.1_ASM1464749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:37,506] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:37,507] [INFO] Found 6/6 markers.
[2024-01-24 11:59:37,547] [INFO] Query marker FASTA was written to GCF_014647495.1_ASM1464749v1_genomic.fna/markers.fasta
[2024-01-24 11:59:37,547] [INFO] Task started: Blastn
[2024-01-24 11:59:37,547] [INFO] Running command: blastn -query GCF_014647495.1_ASM1464749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00022a97-e1d2-4254-914b-c3fb41c8cfaf/dqc_reference/reference_markers.fasta -out GCF_014647495.1_ASM1464749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:38,665] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:38,668] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:38,669] [INFO] Target genome list was writen to GCF_014647495.1_ASM1464749v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:38,674] [INFO] Task started: fastANI
[2024-01-24 11:59:38,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgb848b600-7e42-4c61-8ca1-d06030f2f244/GCF_014647495.1_ASM1464749v1_genomic.fna.gz --refList GCF_014647495.1_ASM1464749v1_genomic.fna/target_genomes.txt --output GCF_014647495.1_ASM1464749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:47,509] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:47,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00022a97-e1d2-4254-914b-c3fb41c8cfaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:47,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00022a97-e1d2-4254-914b-c3fb41c8cfaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:47,524] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:47,525] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:47,525] [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=JCM 1973	GCA_014647495.1	37930	37930	type	True	100.0	1259	1260	95	conclusive
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	99.9966	1257	1260	95	conclusive
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	83.6339	734	1260	95	below_threshold
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	82.9638	738	1260	95	below_threshold
Glutamicibacter mysorens	strain=DSM 12798	GCA_002797775.1	257984	257984	type	True	82.8946	737	1260	95	below_threshold
Glutamicibacter nicotianae	strain=NBRC 14234	GCA_006539525.1	37929	37929	type	True	82.8494	716	1260	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	81.5111	602	1260	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.0067	303	1260	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.9961	305	1260	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.7539	165	1260	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	76.6339	150	1260	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	76.5588	142	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:47,527] [INFO] DFAST Taxonomy check result was written to GCF_014647495.1_ASM1464749v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:47,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:47,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:47,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00022a97-e1d2-4254-914b-c3fb41c8cfaf/dqc_reference/checkm_data
[2024-01-24 11:59:47,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:47,565] [INFO] Task started: CheckM
[2024-01-24 11:59:47,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647495.1_ASM1464749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647495.1_ASM1464749v1_genomic.fna/checkm_input GCF_014647495.1_ASM1464749v1_genomic.fna/checkm_result
[2024-01-24 12:00:23,690] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:23,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:23,717] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:23,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:23,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647495.1_ASM1464749v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:23,720] [INFO] Task started: Blastn
[2024-01-24 12:00:23,720] [INFO] Running command: blastn -query GCF_014647495.1_ASM1464749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00022a97-e1d2-4254-914b-c3fb41c8cfaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647495.1_ASM1464749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:25,472] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:25,477] [INFO] Selected 9 target genomes.
[2024-01-24 12:00:25,478] [INFO] Target genome list was writen to GCF_014647495.1_ASM1464749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:25,486] [INFO] Task started: fastANI
[2024-01-24 12:00:25,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgb848b600-7e42-4c61-8ca1-d06030f2f244/GCF_014647495.1_ASM1464749v1_genomic.fna.gz --refList GCF_014647495.1_ASM1464749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647495.1_ASM1464749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:33,375] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:33,389] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:33,389] [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	100.0	1259	1260	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	91.4406	1068	1260	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	83.6339	734	1260	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	82.8295	718	1260	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	81.9518	686	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.88	98.56	0.94	0.92	3	-
GCF_000197735.1	s__Glutamicibacter arilaitensis	81.8636	677	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.79	97.54	0.91	0.83	7	-
GCF_001302565.1	s__Glutamicibacter halophytocola	81.5133	602	1260	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	81.4207	633	1260	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	81.2964	589	1260	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 12:00:33,390] [INFO] GTDB search result was written to GCF_014647495.1_ASM1464749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:33,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:33,394] [INFO] DFAST_QC result json was written to GCF_014647495.1_ASM1464749v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:33,394] [INFO] DFAST_QC completed!
[2024-01-24 12:00:33,394] [INFO] Total running time: 0h1m10s