[2024-01-25 18:09:35,748] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:35,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:35,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg0481cbcf-0ec2-4a7f-a1ed-91030d21e071/dqc_reference
[2024-01-25 18:09:36,932] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:36,933] [INFO] Task started: Prodigal
[2024-01-25 18:09:36,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg425974eb-55e8-451f-83c2-0397d5c97cf9/GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/cds.fna -a GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:57,617] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:57,618] [INFO] Task started: HMMsearch
[2024-01-25 18:09:57,618] [INFO] Running command: hmmsearch --tblout GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0481cbcf-0ec2-4a7f-a1ed-91030d21e071/dqc_reference/reference_markers.hmm GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:57,999] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:58,000] [INFO] Found 6/6 markers.
[2024-01-25 18:09:58,045] [INFO] Query marker FASTA was written to GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:09:58,045] [INFO] Task started: Blastn
[2024-01-25 18:09:58,045] [INFO] Running command: blastn -query GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0481cbcf-0ec2-4a7f-a1ed-91030d21e071/dqc_reference/reference_markers.fasta -out GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:58,603] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:58,610] [INFO] Selected 12 target genomes.
[2024-01-25 18:09:58,610] [INFO] Target genome list was writen to GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:09:58,621] [INFO] Task started: fastANI
[2024-01-25 18:09:58,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg425974eb-55e8-451f-83c2-0397d5c97cf9/GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna.gz --refList GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:10,540] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:10,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0481cbcf-0ec2-4a7f-a1ed-91030d21e071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:10,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0481cbcf-0ec2-4a7f-a1ed-91030d21e071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:10,549] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:10,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:10,549] [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
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	100.0	1799	1799	95	conclusive
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	81.8453	1039	1799	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	80.7824	868	1799	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	80.4935	800	1799	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	80.4817	838	1799	95	below_threshold
Algoriphagus resistens	strain=NH1	GCA_001442615.1	1750590	1750590	type	True	80.1704	825	1799	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_003254355.1	57028	57028	type	True	79.9188	716	1799	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	79.894	721	1799	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	77.4934	218	1799	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	76.5571	119	1799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:10,550] [INFO] DFAST Taxonomy check result was written to GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:10:10,551] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:10,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:10,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0481cbcf-0ec2-4a7f-a1ed-91030d21e071/dqc_reference/checkm_data
[2024-01-25 18:10:10,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:10,600] [INFO] Task started: CheckM
[2024-01-25 18:10:10,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/checkm_input GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:11:10,316] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:10,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:10,337] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:10,337] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:10,338] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:11:10,338] [INFO] Task started: Blastn
[2024-01-25 18:11:10,338] [INFO] Running command: blastn -query GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0481cbcf-0ec2-4a7f-a1ed-91030d21e071/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:11,123] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:11,125] [INFO] Selected 8 target genomes.
[2024-01-25 18:11:11,125] [INFO] Target genome list was writen to GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:11,132] [INFO] Task started: fastANI
[2024-01-25 18:11:11,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg425974eb-55e8-451f-83c2-0397d5c97cf9/GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna.gz --refList GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:20,433] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:20,440] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:20,440] [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_900116615.1	s__Algoriphagus locisalis	100.0	1799	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003259505.1	s__Algoriphagus yeomjeoni	81.8424	1040	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	80.9007	880	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	80.7848	867	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	80.4889	837	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	80.4861	801	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001442615.1	s__Algoriphagus resistens	80.1786	823	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150505.1	s__Algoriphagus ratkowskyi	79.9055	719	1799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:20,442] [INFO] GTDB search result was written to GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:20,442] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:20,445] [INFO] DFAST_QC result json was written to GCF_900116615.1_IMG-taxon_2639762564_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:11:20,446] [INFO] DFAST_QC completed!
[2024-01-25 18:11:20,446] [INFO] Total running time: 0h1m45s