[2024-01-24 13:48:59,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,152] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc93861e-ee3c-4e2a-89e4-59ea1c449c54/dqc_reference
[2024-01-24 13:49:00,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,459] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bb9a793-8468-469e-b7a2-9a2a8bc91ec6/GCF_009695545.1_ASM969554v1_genomic.fna.gz | prodigal -d GCF_009695545.1_ASM969554v1_genomic.fna/cds.fna -a GCF_009695545.1_ASM969554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:14,495] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:14,496] [INFO] Task started: HMMsearch
[2024-01-24 13:49:14,496] [INFO] Running command: hmmsearch --tblout GCF_009695545.1_ASM969554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc93861e-ee3c-4e2a-89e4-59ea1c449c54/dqc_reference/reference_markers.hmm GCF_009695545.1_ASM969554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:14,795] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:14,797] [INFO] Found 6/6 markers.
[2024-01-24 13:49:14,842] [INFO] Query marker FASTA was written to GCF_009695545.1_ASM969554v1_genomic.fna/markers.fasta
[2024-01-24 13:49:14,843] [INFO] Task started: Blastn
[2024-01-24 13:49:14,843] [INFO] Running command: blastn -query GCF_009695545.1_ASM969554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc93861e-ee3c-4e2a-89e4-59ea1c449c54/dqc_reference/reference_markers.fasta -out GCF_009695545.1_ASM969554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,537] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,541] [INFO] Selected 22 target genomes.
[2024-01-24 13:49:15,542] [INFO] Target genome list was writen to GCF_009695545.1_ASM969554v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:15,551] [INFO] Task started: fastANI
[2024-01-24 13:49:15,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bb9a793-8468-469e-b7a2-9a2a8bc91ec6/GCF_009695545.1_ASM969554v1_genomic.fna.gz --refList GCF_009695545.1_ASM969554v1_genomic.fna/target_genomes.txt --output GCF_009695545.1_ASM969554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:35,604] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:35,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc93861e-ee3c-4e2a-89e4-59ea1c449c54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:35,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc93861e-ee3c-4e2a-89e4-59ea1c449c54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:35,611] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:35,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:35,611] [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
Victivallis lenta	strain=BBE-744-WT-12	GCA_009695545.1	2606640	2606640	type	True	100.0	1806	1809	95	conclusive
Victivallis vadensis	strain=DSM 14823	GCA_003096415.1	172901	172901	type	True	80.6764	589	1809	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	74.7456	57	1809	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	74.742	55	1809	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	74.7095	80	1809	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:35,613] [INFO] DFAST Taxonomy check result was written to GCF_009695545.1_ASM969554v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:35,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:35,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:35,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc93861e-ee3c-4e2a-89e4-59ea1c449c54/dqc_reference/checkm_data
[2024-01-24 13:49:35,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:35,674] [INFO] Task started: CheckM
[2024-01-24 13:49:35,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695545.1_ASM969554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695545.1_ASM969554v1_genomic.fna/checkm_input GCF_009695545.1_ASM969554v1_genomic.fna/checkm_result
[2024-01-24 13:50:21,247] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:21,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,265] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:21,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:21,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695545.1_ASM969554v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:21,266] [INFO] Task started: Blastn
[2024-01-24 13:50:21,267] [INFO] Running command: blastn -query GCF_009695545.1_ASM969554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc93861e-ee3c-4e2a-89e4-59ea1c449c54/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695545.1_ASM969554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:22,531] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:22,533] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:22,533] [INFO] Target genome list was writen to GCF_009695545.1_ASM969554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:22,556] [INFO] Task started: fastANI
[2024-01-24 13:50:22,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bb9a793-8468-469e-b7a2-9a2a8bc91ec6/GCF_009695545.1_ASM969554v1_genomic.fna.gz --refList GCF_009695545.1_ASM969554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695545.1_ASM969554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:29,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:29,854] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:29,855] [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_009695545.1	s__Victivallis lenta	100.0	1806	1809	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.99	98.42	0.92	0.87	10	conclusive
GCA_018265615.1	s__Victivallis sp018265615	81.7529	838	1809	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096415.1	s__Victivallis vadensis	80.7035	586	1809	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.78	98.45	0.89	0.85	7	-
GCA_900551245.1	s__Victivallis sp900551245	79.5988	408	1809	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.16	98.16	0.84	0.84	2	-
GCA_900768515.1	s__Victivallis sp900768515	78.8039	359	1809	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	99.40	99.40	0.89	0.89	2	-
GCA_900550905.1	s__Victivallis sp900550905	78.6117	360	1809	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017450705.1	s__UBA1784 sp017450705	76.5091	138	1809	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__UBA1784	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:29,856] [INFO] GTDB search result was written to GCF_009695545.1_ASM969554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:29,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:29,859] [INFO] DFAST_QC result json was written to GCF_009695545.1_ASM969554v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:29,859] [INFO] DFAST_QC completed!
[2024-01-24 13:50:29,859] [INFO] Total running time: 0h1m31s