[2024-01-24 13:27:42,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:42,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:42,588] [INFO] DQC Reference Directory: /var/lib/cwl/stgbce8203c-1d57-485e-8820-d9695eb08ec4/dqc_reference
[2024-01-24 13:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:43,883] [INFO] Task started: Prodigal
[2024-01-24 13:27:43,883] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb6deb60-ac50-4944-88f7-4c7e3e10a583/GCF_000009905.1_ASM990v1_genomic.fna.gz | prodigal -d GCF_000009905.1_ASM990v1_genomic.fna/cds.fna -a GCF_000009905.1_ASM990v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:54,840] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:54,840] [INFO] Task started: HMMsearch
[2024-01-24 13:27:54,841] [INFO] Running command: hmmsearch --tblout GCF_000009905.1_ASM990v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbce8203c-1d57-485e-8820-d9695eb08ec4/dqc_reference/reference_markers.hmm GCF_000009905.1_ASM990v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:55,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:55,143] [INFO] Found 6/6 markers.
[2024-01-24 13:27:55,186] [INFO] Query marker FASTA was written to GCF_000009905.1_ASM990v1_genomic.fna/markers.fasta
[2024-01-24 13:27:55,186] [INFO] Task started: Blastn
[2024-01-24 13:27:55,186] [INFO] Running command: blastn -query GCF_000009905.1_ASM990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbce8203c-1d57-485e-8820-d9695eb08ec4/dqc_reference/reference_markers.fasta -out GCF_000009905.1_ASM990v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:55,886] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:55,889] [INFO] Selected 18 target genomes.
[2024-01-24 13:27:55,890] [INFO] Target genome list was writen to GCF_000009905.1_ASM990v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:55,907] [INFO] Task started: fastANI
[2024-01-24 13:27:55,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb6deb60-ac50-4944-88f7-4c7e3e10a583/GCF_000009905.1_ASM990v1_genomic.fna.gz --refList GCF_000009905.1_ASM990v1_genomic.fna/target_genomes.txt --output GCF_000009905.1_ASM990v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:12,202] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:12,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbce8203c-1d57-485e-8820-d9695eb08ec4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:12,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbce8203c-1d57-485e-8820-d9695eb08ec4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:12,213] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:12,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:12,214] [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
Symbiobacterium thermophilum	strain=IAM14863	GCA_000009905.1	2734	2734	type	True	100.0	1188	1188	95	conclusive
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	82.7524	826	1188	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	76.7433	144	1188	95	below_threshold
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	76.5236	141	1188	95	below_threshold
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	76.1749	55	1188	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	75.2525	64	1188	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.2449	157	1188	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.0436	93	1188	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	75.0325	114	1188	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	74.9849	120	1188	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	74.9538	139	1188	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	74.9468	154	1188	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	74.882	129	1188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:12,215] [INFO] DFAST Taxonomy check result was written to GCF_000009905.1_ASM990v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:12,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:12,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:12,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbce8203c-1d57-485e-8820-d9695eb08ec4/dqc_reference/checkm_data
[2024-01-24 13:28:12,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:12,258] [INFO] Task started: CheckM
[2024-01-24 13:28:12,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000009905.1_ASM990v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000009905.1_ASM990v1_genomic.fna/checkm_input GCF_000009905.1_ASM990v1_genomic.fna/checkm_result
[2024-01-24 13:28:47,947] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:47,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:47,973] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:47,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:47,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000009905.1_ASM990v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:47,974] [INFO] Task started: Blastn
[2024-01-24 13:28:47,974] [INFO] Running command: blastn -query GCF_000009905.1_ASM990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbce8203c-1d57-485e-8820-d9695eb08ec4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000009905.1_ASM990v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:49,098] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:49,102] [INFO] Selected 16 target genomes.
[2024-01-24 13:28:49,102] [INFO] Target genome list was writen to GCF_000009905.1_ASM990v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:49,136] [INFO] Task started: fastANI
[2024-01-24 13:28:49,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb6deb60-ac50-4944-88f7-4c7e3e10a583/GCF_000009905.1_ASM990v1_genomic.fna.gz --refList GCF_000009905.1_ASM990v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000009905.1_ASM990v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:59,320] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:59,335] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:59,335] [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_000009905.1	s__Symbiobacterium thermophilum	100.0	1188	1188	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003242675.1	s__Symbiobacterium sp003242675	86.7688	740	1188	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874315.1	s__Symbiobacterium terraclitae	82.7126	830	1188	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242505.1	s__ZC4RG38 sp003242505	77.1022	204	1188	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__ZC4RG38;g__ZC4RG38	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183545.2	s__Thermaerobacter subterraneus	76.5225	142	1188	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	95.08	95.08	0.91	0.91	2	-
GCA_902809825.1	s__R501 sp902809825	75.5119	80	1188	d__Bacteria;p__Firmicutes_E;c__Sulfobacillia;o__Sulfobacillales;f__R501;g__R501	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016615955.1	s__Luteimonas sp016615955	75.2736	78	1188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.39	98.78	0.97	0.95	3	-
GCA_018606725.1	s__JAGYID01 sp018606725	74.9948	63	1188	d__Bacteria;p__Acidobacteriota;c__Mor1;o__Gp22-AA2;f__Gp22-AA2;g__JAGYID01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003558435.1	s__PWLR01 sp003558435	74.8421	55	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__PWLR01	95.0	99.63	99.63	0.94	0.94	2	-
GCA_019239425.1	s__QHXN01 sp019239425	74.8397	78	1188	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002753665.1	s__DC0425bin3 sp002753665	74.8112	52	1188	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__DC0425bin3;g__DC0425bin3	95.0	99.96	99.96	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,337] [INFO] GTDB search result was written to GCF_000009905.1_ASM990v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:59,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:59,341] [INFO] DFAST_QC result json was written to GCF_000009905.1_ASM990v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:59,341] [INFO] DFAST_QC completed!
[2024-01-24 13:28:59,341] [INFO] Total running time: 0h1m17s