[2024-01-25 19:05:50,425] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:50,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:50,427] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0ffed78-9da2-4529-9121-17ea2bacdb27/dqc_reference
[2024-01-25 19:05:51,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:51,585] [INFO] Task started: Prodigal
[2024-01-25 19:05:51,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg91933976-480e-4f6a-a5fe-1bf39e57cf1e/GCF_030161255.1_ASM3016125v1_genomic.fna.gz | prodigal -d GCF_030161255.1_ASM3016125v1_genomic.fna/cds.fna -a GCF_030161255.1_ASM3016125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:06,026] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:06,026] [INFO] Task started: HMMsearch
[2024-01-25 19:06:06,026] [INFO] Running command: hmmsearch --tblout GCF_030161255.1_ASM3016125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0ffed78-9da2-4529-9121-17ea2bacdb27/dqc_reference/reference_markers.hmm GCF_030161255.1_ASM3016125v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:06,393] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:06,394] [INFO] Found 6/6 markers.
[2024-01-25 19:06:06,434] [INFO] Query marker FASTA was written to GCF_030161255.1_ASM3016125v1_genomic.fna/markers.fasta
[2024-01-25 19:06:06,434] [INFO] Task started: Blastn
[2024-01-25 19:06:06,434] [INFO] Running command: blastn -query GCF_030161255.1_ASM3016125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0ffed78-9da2-4529-9121-17ea2bacdb27/dqc_reference/reference_markers.fasta -out GCF_030161255.1_ASM3016125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:07,393] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:07,396] [INFO] Selected 18 target genomes.
[2024-01-25 19:06:07,396] [INFO] Target genome list was writen to GCF_030161255.1_ASM3016125v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:07,405] [INFO] Task started: fastANI
[2024-01-25 19:06:07,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg91933976-480e-4f6a-a5fe-1bf39e57cf1e/GCF_030161255.1_ASM3016125v1_genomic.fna.gz --refList GCF_030161255.1_ASM3016125v1_genomic.fna/target_genomes.txt --output GCF_030161255.1_ASM3016125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:25,520] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:25,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0ffed78-9da2-4529-9121-17ea2bacdb27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:25,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0ffed78-9da2-4529-9121-17ea2bacdb27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:25,532] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:06:25,532] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:06:25,532] [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
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	85.3438	936	1533	95	below_threshold
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	83.641	968	1533	95	below_threshold
Zoogloea oleivorans	strain=Buc	GCA_008107625.1	1552750	1552750	type	True	83.5144	958	1533	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	80.5957	525	1533	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	80.4628	532	1533	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	80.4436	545	1533	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	80.2304	590	1533	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	79.7702	586	1533	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	79.7407	460	1533	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	79.5169	490	1533	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.4615	565	1533	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	79.4581	516	1533	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.3362	529	1533	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	79.1816	590	1533	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	79.1384	578	1533	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.8206	351	1533	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	76.6562	281	1533	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	76.6303	271	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:25,533] [INFO] DFAST Taxonomy check result was written to GCF_030161255.1_ASM3016125v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:25,535] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:25,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:25,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0ffed78-9da2-4529-9121-17ea2bacdb27/dqc_reference/checkm_data
[2024-01-25 19:06:25,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:25,583] [INFO] Task started: CheckM
[2024-01-25 19:06:25,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161255.1_ASM3016125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161255.1_ASM3016125v1_genomic.fna/checkm_input GCF_030161255.1_ASM3016125v1_genomic.fna/checkm_result
[2024-01-25 19:07:16,091] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:16,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.03%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:16,118] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:16,118] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:16,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161255.1_ASM3016125v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:16,118] [INFO] Task started: Blastn
[2024-01-25 19:07:16,118] [INFO] Running command: blastn -query GCF_030161255.1_ASM3016125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0ffed78-9da2-4529-9121-17ea2bacdb27/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161255.1_ASM3016125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:18,016] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:18,020] [INFO] Selected 13 target genomes.
[2024-01-25 19:07:18,020] [INFO] Target genome list was writen to GCF_030161255.1_ASM3016125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:18,033] [INFO] Task started: fastANI
[2024-01-25 19:07:18,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg91933976-480e-4f6a-a5fe-1bf39e57cf1e/GCF_030161255.1_ASM3016125v1_genomic.fna.gz --refList GCF_030161255.1_ASM3016125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161255.1_ASM3016125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:33,078] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:33,086] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:33,087] [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_009469605.1	s__Zoogloea sp009469605	95.95	1286	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015657735.1	s__Zoogloea sp015657735	85.4854	682	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539865.1	s__Zoogloea ramigera	85.3462	936	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	99.03	99.03	0.93	0.93	2	-
GCA_016789125.1	s__Zoogloea sp016789125	85.0337	709	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720685.1	s__Zoogloea sp016720685	84.3116	874	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927165.1	s__Zoogloea sp012927165	83.5984	971	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241665.1	s__Zoogloea sp018241665	83.598	883	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026175.1	s__Zoogloea sp009026175	83.5834	862	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002028455.1	s__Zoogloea sp002028455	83.5414	932	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309145.1	s__Zoogloea sp017309145	83.3324	754	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241685.1	s__Zoogloea sp018241685	83.1583	898	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703645.1	s__Zoogloea sp008011925	83.114	882	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	98.96	98.57	0.96	0.92	4	-
GCA_018241725.1	s__Zoogloea sp018241725	83.107	878	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:33,088] [INFO] GTDB search result was written to GCF_030161255.1_ASM3016125v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:33,089] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:33,092] [INFO] DFAST_QC result json was written to GCF_030161255.1_ASM3016125v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:33,092] [INFO] DFAST_QC completed!
[2024-01-25 19:07:33,092] [INFO] Total running time: 0h1m43s