[2024-01-24 14:14:37,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg80d8d9ba-1799-4ac2-947c-7e2e051930bb/dqc_reference
[2024-01-24 14:14:38,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,877] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg18ac2003-8706-4e87-9d20-a61f61b644fb/GCF_004310865.1_ASM431086v1_genomic.fna.gz | prodigal -d GCF_004310865.1_ASM431086v1_genomic.fna/cds.fna -a GCF_004310865.1_ASM431086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:54,551] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:54,551] [INFO] Task started: HMMsearch
[2024-01-24 14:14:54,551] [INFO] Running command: hmmsearch --tblout GCF_004310865.1_ASM431086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80d8d9ba-1799-4ac2-947c-7e2e051930bb/dqc_reference/reference_markers.hmm GCF_004310865.1_ASM431086v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:54,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:54,858] [INFO] Found 6/6 markers.
[2024-01-24 14:14:54,901] [INFO] Query marker FASTA was written to GCF_004310865.1_ASM431086v1_genomic.fna/markers.fasta
[2024-01-24 14:14:54,902] [INFO] Task started: Blastn
[2024-01-24 14:14:54,902] [INFO] Running command: blastn -query GCF_004310865.1_ASM431086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80d8d9ba-1799-4ac2-947c-7e2e051930bb/dqc_reference/reference_markers.fasta -out GCF_004310865.1_ASM431086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:56,078] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:56,081] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:56,082] [INFO] Target genome list was writen to GCF_004310865.1_ASM431086v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:56,086] [INFO] Task started: fastANI
[2024-01-24 14:14:56,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ac2003-8706-4e87-9d20-a61f61b644fb/GCF_004310865.1_ASM431086v1_genomic.fna.gz --refList GCF_004310865.1_ASM431086v1_genomic.fna/target_genomes.txt --output GCF_004310865.1_ASM431086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:06,862] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:06,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80d8d9ba-1799-4ac2-947c-7e2e051930bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:06,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80d8d9ba-1799-4ac2-947c-7e2e051930bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:06,873] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:06,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:06,873] [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
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	100.0	1275	1275	95	conclusive
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	82.5433	682	1275	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	82.406	737	1275	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	82.349	678	1275	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	82.1438	669	1275	95	below_threshold
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	81.697	627	1275	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.8125	519	1275	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.7754	482	1275	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.7468	478	1275	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.5443	475	1275	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.0993	470	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:06,875] [INFO] DFAST Taxonomy check result was written to GCF_004310865.1_ASM431086v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:06,877] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:06,877] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:06,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80d8d9ba-1799-4ac2-947c-7e2e051930bb/dqc_reference/checkm_data
[2024-01-24 14:15:06,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:06,923] [INFO] Task started: CheckM
[2024-01-24 14:15:06,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004310865.1_ASM431086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004310865.1_ASM431086v1_genomic.fna/checkm_input GCF_004310865.1_ASM431086v1_genomic.fna/checkm_result
[2024-01-24 14:17:16,716] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:16,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:16,749] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:16,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:16,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004310865.1_ASM431086v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:16,751] [INFO] Task started: Blastn
[2024-01-24 14:17:16,751] [INFO] Running command: blastn -query GCF_004310865.1_ASM431086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80d8d9ba-1799-4ac2-947c-7e2e051930bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_004310865.1_ASM431086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:21,161] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:21,164] [INFO] Selected 16 target genomes.
[2024-01-24 14:17:21,165] [INFO] Target genome list was writen to GCF_004310865.1_ASM431086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:21,194] [INFO] Task started: fastANI
[2024-01-24 14:17:21,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ac2003-8706-4e87-9d20-a61f61b644fb/GCF_004310865.1_ASM431086v1_genomic.fna.gz --refList GCF_004310865.1_ASM431086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004310865.1_ASM431086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:37,651] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:37,664] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:37,665] [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_004310865.1	s__Aquabacterium lacunae	100.0	1275	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001770725.1	s__Aquabacterium sp001770725	82.777	719	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447195.1	s__Aquabacterium parvum	82.5915	678	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.32	96.21	0.91	0.89	4	-
GCA_019112875.1	s__Aquabacterium excrementipullorum	82.5895	703	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502875.1	s__Aquabacterium sp005502875	82.4799	669	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933735.1	s__Aquabacterium sp003933735	82.3878	738	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362855.1	s__Aquabacterium commune	82.376	676	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	95.44	95.44	0.90	0.90	2	-
GCA_002339015.1	s__Aquabacterium sp002339015	82.1726	657	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.88	99.88	0.91	0.91	2	-
GCF_003100395.1	s__Aquabacterium olei	82.1527	668	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894125.1	s__Aquabacterium sp903894125	82.0556	465	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.35	99.35	0.82	0.82	2	-
GCA_017989885.1	s__Aquabacterium sp017989885	82.0439	329	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	98.47	98.47	0.69	0.69	2	-
GCA_016195855.1	s__Aquabacterium sp016195855	81.829	670	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768065.1	s__Aquabacterium sp000768065	81.815	709	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909205.1	s__Aquabacterium fontiphilum	81.7181	626	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185075.1	s__Aquabacterium sp016185075	81.4512	485	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963115.1	s__Aquabacterium sp003963115	81.4308	651	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:37,666] [INFO] GTDB search result was written to GCF_004310865.1_ASM431086v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:37,667] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:37,671] [INFO] DFAST_QC result json was written to GCF_004310865.1_ASM431086v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:37,671] [INFO] DFAST_QC completed!
[2024-01-24 14:17:37,671] [INFO] Total running time: 0h3m0s