[2024-01-24 11:26:20,786] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf707959-1767-4de3-b00c-69a07d56194c/dqc_reference
[2024-01-24 11:26:22,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,020] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg64654afe-1b06-4b4e-997a-ec54c6f888c5/GCF_016583525.1_ASM1658352v1_genomic.fna.gz | prodigal -d GCF_016583525.1_ASM1658352v1_genomic.fna/cds.fna -a GCF_016583525.1_ASM1658352v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:35,379] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:35,380] [INFO] Task started: HMMsearch
[2024-01-24 11:26:35,380] [INFO] Running command: hmmsearch --tblout GCF_016583525.1_ASM1658352v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf707959-1767-4de3-b00c-69a07d56194c/dqc_reference/reference_markers.hmm GCF_016583525.1_ASM1658352v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:35,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:35,737] [INFO] Found 6/6 markers.
[2024-01-24 11:26:35,788] [INFO] Query marker FASTA was written to GCF_016583525.1_ASM1658352v1_genomic.fna/markers.fasta
[2024-01-24 11:26:35,788] [INFO] Task started: Blastn
[2024-01-24 11:26:35,788] [INFO] Running command: blastn -query GCF_016583525.1_ASM1658352v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf707959-1767-4de3-b00c-69a07d56194c/dqc_reference/reference_markers.fasta -out GCF_016583525.1_ASM1658352v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:36,934] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:36,937] [INFO] Selected 12 target genomes.
[2024-01-24 11:26:36,938] [INFO] Target genome list was writen to GCF_016583525.1_ASM1658352v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:36,943] [INFO] Task started: fastANI
[2024-01-24 11:26:36,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg64654afe-1b06-4b4e-997a-ec54c6f888c5/GCF_016583525.1_ASM1658352v1_genomic.fna.gz --refList GCF_016583525.1_ASM1658352v1_genomic.fna/target_genomes.txt --output GCF_016583525.1_ASM1658352v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:53,976] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:53,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf707959-1767-4de3-b00c-69a07d56194c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:53,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf707959-1767-4de3-b00c-69a07d56194c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:53,989] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:53,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:53,989] [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
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	100.0	1632	1640	95	conclusive
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	99.9886	1623	1640	95	conclusive
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	92.9947	1195	1640	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	92.9252	1141	1640	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	81.013	719	1640	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.7602	740	1640	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.3803	716	1640	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	80.3424	895	1640	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.2697	681	1640	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.1419	876	1640	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.4312	680	1640	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.2067	639	1640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:53,991] [INFO] DFAST Taxonomy check result was written to GCF_016583525.1_ASM1658352v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:53,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:53,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:53,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf707959-1767-4de3-b00c-69a07d56194c/dqc_reference/checkm_data
[2024-01-24 11:26:53,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:54,045] [INFO] Task started: CheckM
[2024-01-24 11:26:54,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583525.1_ASM1658352v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583525.1_ASM1658352v1_genomic.fna/checkm_input GCF_016583525.1_ASM1658352v1_genomic.fna/checkm_result
[2024-01-24 11:28:02,016] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:02,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:02,038] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:02,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:02,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583525.1_ASM1658352v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:02,039] [INFO] Task started: Blastn
[2024-01-24 11:28:02,040] [INFO] Running command: blastn -query GCF_016583525.1_ASM1658352v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf707959-1767-4de3-b00c-69a07d56194c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583525.1_ASM1658352v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:04,285] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:04,289] [INFO] Selected 9 target genomes.
[2024-01-24 11:28:04,290] [INFO] Target genome list was writen to GCF_016583525.1_ASM1658352v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:04,299] [INFO] Task started: fastANI
[2024-01-24 11:28:04,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg64654afe-1b06-4b4e-997a-ec54c6f888c5/GCF_016583525.1_ASM1658352v1_genomic.fna.gz --refList GCF_016583525.1_ASM1658352v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583525.1_ASM1658352v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:18,338] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:18,354] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:18,355] [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_004340905.1	s__Rubrivivax gelatinosus	99.9886	1623	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000284255.1	s__Rubrivivax gelatinosus_A	93.1461	1378	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	92.9703	1138	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCF_016583785.1	s__Rubrivivax gelatinosus_B	90.116	1312	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.02	99.02	0.92	0.92	2	-
GCA_001725505.1	s__Rubrivivax sp001725505	82.7451	700	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	81.6772	826	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCA_018971105.1	s__Rubrivivax sp018971105	81.623	714	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	81.1912	641	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223165.1	s__Rubrivivax sp016223165	80.5376	903	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:18,357] [INFO] GTDB search result was written to GCF_016583525.1_ASM1658352v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:18,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:18,362] [INFO] DFAST_QC result json was written to GCF_016583525.1_ASM1658352v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:18,362] [INFO] DFAST_QC completed!
[2024-01-24 11:28:18,362] [INFO] Total running time: 0h1m58s