[2024-01-24 13:17:03,642] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:03,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:03,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dc348a9-77ec-4353-8ff6-dce6f37891a9/dqc_reference
[2024-01-24 13:17:04,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:04,956] [INFO] Task started: Prodigal
[2024-01-24 13:17:04,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg0affc9e9-e819-4202-99a5-ed199e31bf2a/GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/cds.fna -a GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:11,742] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:11,742] [INFO] Task started: HMMsearch
[2024-01-24 13:17:11,742] [INFO] Running command: hmmsearch --tblout GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dc348a9-77ec-4353-8ff6-dce6f37891a9/dqc_reference/reference_markers.hmm GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:12,019] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:12,021] [INFO] Found 6/6 markers.
[2024-01-24 13:17:12,054] [INFO] Query marker FASTA was written to GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:17:12,055] [INFO] Task started: Blastn
[2024-01-24 13:17:12,055] [INFO] Running command: blastn -query GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc348a9-77ec-4353-8ff6-dce6f37891a9/dqc_reference/reference_markers.fasta -out GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:12,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:12,755] [INFO] Selected 23 target genomes.
[2024-01-24 13:17:12,755] [INFO] Target genome list was writen to GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:17:12,765] [INFO] Task started: fastANI
[2024-01-24 13:17:12,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg0affc9e9-e819-4202-99a5-ed199e31bf2a/GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna.gz --refList GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:23,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:23,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dc348a9-77ec-4353-8ff6-dce6f37891a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:23,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dc348a9-77ec-4353-8ff6-dce6f37891a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:23,814] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:23,815] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:23,815] [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
Pseudobutyrivibrio ruminis	strain=DSM 9787	GCA_900218035.1	46206	46206	suspected-type	True	100.0	994	996	95	conclusive
Pseudobutyrivibrio xylanivorans	strain=DSM 14809	GCA_900141825.1	185007	185007	type	True	81.6429	464	996	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	78.0507	50	996	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	77.7506	64	996	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.7144	50	996	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	77.4933	54	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:23,816] [INFO] DFAST Taxonomy check result was written to GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:17:23,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:23,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:23,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dc348a9-77ec-4353-8ff6-dce6f37891a9/dqc_reference/checkm_data
[2024-01-24 13:17:23,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:23,857] [INFO] Task started: CheckM
[2024-01-24 13:17:23,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/checkm_input GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:17:51,346] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:51,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:51,373] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:51,374] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:51,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:17:51,375] [INFO] Task started: Blastn
[2024-01-24 13:17:51,375] [INFO] Running command: blastn -query GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc348a9-77ec-4353-8ff6-dce6f37891a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:52,424] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:52,428] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:52,428] [INFO] Target genome list was writen to GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:52,478] [INFO] Task started: fastANI
[2024-01-24 13:17:52,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg0affc9e9-e819-4202-99a5-ed199e31bf2a/GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna.gz --refList GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:59,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:59,915] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:59,915] [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_900218035.1	s__Pseudobutyrivibrio ruminis	100.0	994	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	96.30	96.03	0.86	0.83	5	conclusive
GCA_015057245.1	s__Pseudobutyrivibrio ruminis_E	94.474	794	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000703005.1	s__Pseudobutyrivibrio ruminis_A	93.7747	794	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113655.1	s__Pseudobutyrivibrio sp900113655	82.4514	503	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424305.1	s__Pseudobutyrivibrio ruminis_B	82.1674	479	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775195.1	s__Pseudobutyrivibrio sp902775195	81.7706	385	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621865.1	s__Pseudobutyrivibrio sp000621865	81.7137	504	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100545.1	s__Pseudobutyrivibrio sp900100545	81.6813	467	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	98.38	98.38	0.86	0.86	2	-
GCF_900141825.1	s__Pseudobutyrivibrio xylanivorans	81.6478	465	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057315.1	s__Pseudobutyrivibrio ruminis_D	81.4219	462	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	96.62	96.62	0.81	0.81	2	-
GCF_010906925.1	s__Pseudobutyrivibrio sp900112855	81.181	430	996	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pseudobutyrivibrio	95.0	97.62	96.80	0.89	0.81	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:59,917] [INFO] GTDB search result was written to GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:59,917] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:59,920] [INFO] DFAST_QC result json was written to GCF_900218035.1_IMG-taxon_2596583532_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:17:59,920] [INFO] DFAST_QC completed!
[2024-01-24 13:17:59,921] [INFO] Total running time: 0h0m56s