[2024-01-24 13:56:25,095] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:25,096] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:25,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg882948a4-3699-42d3-bd7c-bf8d33117f27/dqc_reference
[2024-01-24 13:56:26,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:26,381] [INFO] Task started: Prodigal
[2024-01-24 13:56:26,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg28b454dc-3440-480e-86c0-5bfb8b53d374/GCF_000390185.1_Lulo1_genomic.fna.gz | prodigal -d GCF_000390185.1_Lulo1_genomic.fna/cds.fna -a GCF_000390185.1_Lulo1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:54,502] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:54,502] [INFO] Task started: HMMsearch
[2024-01-24 13:56:54,503] [INFO] Running command: hmmsearch --tblout GCF_000390185.1_Lulo1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg882948a4-3699-42d3-bd7c-bf8d33117f27/dqc_reference/reference_markers.hmm GCF_000390185.1_Lulo1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:54,802] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:54,803] [INFO] Found 6/6 markers.
[2024-01-24 13:56:54,847] [INFO] Query marker FASTA was written to GCF_000390185.1_Lulo1_genomic.fna/markers.fasta
[2024-01-24 13:56:54,847] [INFO] Task started: Blastn
[2024-01-24 13:56:54,847] [INFO] Running command: blastn -query GCF_000390185.1_Lulo1_genomic.fna/markers.fasta -db /var/lib/cwl/stg882948a4-3699-42d3-bd7c-bf8d33117f27/dqc_reference/reference_markers.fasta -out GCF_000390185.1_Lulo1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:55,449] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:55,452] [INFO] Selected 21 target genomes.
[2024-01-24 13:56:55,452] [INFO] Target genome list was writen to GCF_000390185.1_Lulo1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:55,466] [INFO] Task started: fastANI
[2024-01-24 13:56:55,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg28b454dc-3440-480e-86c0-5bfb8b53d374/GCF_000390185.1_Lulo1_genomic.fna.gz --refList GCF_000390185.1_Lulo1_genomic.fna/target_genomes.txt --output GCF_000390185.1_Lulo1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:11,649] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:11,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg882948a4-3699-42d3-bd7c-bf8d33117f27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:11,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg882948a4-3699-42d3-bd7c-bf8d33117f27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:11,658] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:11,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:11,659] [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
Lunatimonas lonarensis	strain=AK24	GCA_000390185.1	1232681	1232681	type	True	100.0	1736	1739	95	conclusive
Lunatimonas salinarum	strain=KCTC 42988	GCA_017811155.1	1774590	1774590	type	True	80.6913	610	1739	95	below_threshold
Lunatibacter salilacus	strain=CUG 91308	GCA_009797935.1	2483804	2483804	type	True	77.0913	180	1739	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	76.546	140	1739	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	76.5443	59	1739	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	76.3399	61	1739	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	76.3311	69	1739	95	below_threshold
Cyclobacterium lianum	strain=CGMCC 1.6102	GCA_900143075.1	388280	388280	type	True	76.0595	118	1739	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	76.0491	140	1739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:11,660] [INFO] DFAST Taxonomy check result was written to GCF_000390185.1_Lulo1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:11,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:11,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:11,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg882948a4-3699-42d3-bd7c-bf8d33117f27/dqc_reference/checkm_data
[2024-01-24 13:57:11,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:11,725] [INFO] Task started: CheckM
[2024-01-24 13:57:11,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000390185.1_Lulo1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000390185.1_Lulo1_genomic.fna/checkm_input GCF_000390185.1_Lulo1_genomic.fna/checkm_result
[2024-01-24 13:58:32,184] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:32,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:32,203] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:32,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:32,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000390185.1_Lulo1_genomic.fna/markers.fasta)
[2024-01-24 13:58:32,204] [INFO] Task started: Blastn
[2024-01-24 13:58:32,205] [INFO] Running command: blastn -query GCF_000390185.1_Lulo1_genomic.fna/markers.fasta -db /var/lib/cwl/stg882948a4-3699-42d3-bd7c-bf8d33117f27/dqc_reference/reference_markers_gtdb.fasta -out GCF_000390185.1_Lulo1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:32,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:32,981] [INFO] Selected 26 target genomes.
[2024-01-24 13:58:32,981] [INFO] Target genome list was writen to GCF_000390185.1_Lulo1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:33,019] [INFO] Task started: fastANI
[2024-01-24 13:58:33,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg28b454dc-3440-480e-86c0-5bfb8b53d374/GCF_000390185.1_Lulo1_genomic.fna.gz --refList GCF_000390185.1_Lulo1_genomic.fna/target_genomes_gtdb.txt --output GCF_000390185.1_Lulo1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:52,073] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:52,085] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:52,086] [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_000390185.1	s__Lunatimonas lonarensis	100.0	1736	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017811155.1	s__Lunatimonas salinarum	80.6939	610	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124425.1	s__Lunatimonas sp016124425	76.9989	140	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	76.9585	115	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565295.1	s__Negadavirga sp003565295	76.7207	116	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Negadavirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526355.1	s__Algoriphagus marincola_A	76.4276	50	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014324365.1	s__Algoriphagus sp014324365	76.3425	53	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253485.1	s__Algoriphagus aquaeductus	76.3311	69	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254915.1	s__Algoriphagus sp017254915	76.2481	77	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762705.1	s__Cyclobacterium sp014762705	76.2432	118	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143075.1	s__Cyclobacterium lianum	76.0595	118	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	76.0491	140	1739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:52,088] [INFO] GTDB search result was written to GCF_000390185.1_Lulo1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:52,088] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:52,092] [INFO] DFAST_QC result json was written to GCF_000390185.1_Lulo1_genomic.fna/dqc_result.json
[2024-01-24 13:58:52,092] [INFO] DFAST_QC completed!
[2024-01-24 13:58:52,092] [INFO] Total running time: 0h2m27s