[2024-01-24 13:25:28,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:28,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:28,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg95293af1-29fc-48d6-8009-d976dd6b7fe8/dqc_reference
[2024-01-24 13:25:29,508] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:29,509] [INFO] Task started: Prodigal
[2024-01-24 13:25:29,509] [INFO] Running command: gunzip -c /var/lib/cwl/stgd855d73d-0908-41e0-86d6-66ca37ff86cd/GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/cds.fna -a GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:42,455] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:42,456] [INFO] Task started: HMMsearch
[2024-01-24 13:25:42,456] [INFO] Running command: hmmsearch --tblout GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95293af1-29fc-48d6-8009-d976dd6b7fe8/dqc_reference/reference_markers.hmm GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:42,731] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:42,732] [INFO] Found 6/6 markers.
[2024-01-24 13:25:42,772] [INFO] Query marker FASTA was written to GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:25:42,773] [INFO] Task started: Blastn
[2024-01-24 13:25:42,773] [INFO] Running command: blastn -query GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg95293af1-29fc-48d6-8009-d976dd6b7fe8/dqc_reference/reference_markers.fasta -out GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:43,911] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:43,915] [INFO] Selected 14 target genomes.
[2024-01-24 13:25:43,916] [INFO] Target genome list was writen to GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:25:43,921] [INFO] Task started: fastANI
[2024-01-24 13:25:43,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgd855d73d-0908-41e0-86d6-66ca37ff86cd/GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna.gz --refList GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:56,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:56,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95293af1-29fc-48d6-8009-d976dd6b7fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:56,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95293af1-29fc-48d6-8009-d976dd6b7fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:56,082] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:56,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:56,082] [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
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	100.0	1428	1428	95	conclusive
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	81.7913	817	1428	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	81.6442	809	1428	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	81.6117	823	1428	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	80.089	679	1428	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	79.6978	594	1428	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	79.2198	533	1428	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	79.1757	548	1428	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.6453	549	1428	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.3272	449	1428	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.1968	420	1428	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.1454	408	1428	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9656	412	1428	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4882	346	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:56,084] [INFO] DFAST Taxonomy check result was written to GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:25:56,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:56,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:56,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95293af1-29fc-48d6-8009-d976dd6b7fe8/dqc_reference/checkm_data
[2024-01-24 13:25:56,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:56,143] [INFO] Task started: CheckM
[2024-01-24 13:25:56,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/checkm_input GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 13:26:40,337] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:40,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:40,368] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:40,368] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:40,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:26:40,369] [INFO] Task started: Blastn
[2024-01-24 13:26:40,369] [INFO] Running command: blastn -query GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg95293af1-29fc-48d6-8009-d976dd6b7fe8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:42,587] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:42,591] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:42,591] [INFO] Target genome list was writen to GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:42,602] [INFO] Task started: fastANI
[2024-01-24 13:26:42,603] [INFO] Running command: fastANI --query /var/lib/cwl/stgd855d73d-0908-41e0-86d6-66ca37ff86cd/GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna.gz --refList GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:52,266] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:52,275] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:52,275] [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_900172265.1	s__Roseivivax jejudonensis	100.0	1428	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112685.1	s__Roseivivax sediminis	82.586	892	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	81.8143	815	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCF_000521785.1	s__Roseivivax halodurans	81.635	810	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	81.6092	823	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	79.677	600	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	78.8504	582	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	78.4825	546	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	77.9263	421	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447385.1	s__Paracoccus sp001447385	77.4431	385	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:52,277] [INFO] GTDB search result was written to GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:52,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:52,281] [INFO] DFAST_QC result json was written to GCF_900172265.1_R.jejudonensis_CECT8625_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:26:52,281] [INFO] DFAST_QC completed!
[2024-01-24 13:26:52,281] [INFO] Total running time: 0h1m24s