[2024-01-24 13:25:29,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a72cf8d-9cc3-4b06-9855-990be917cf75/dqc_reference
[2024-01-24 13:25:31,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,100] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg230e902d-372e-497c-b9f3-4ed9743506db/GCF_005217605.1_ASM521760v1_genomic.fna.gz | prodigal -d GCF_005217605.1_ASM521760v1_genomic.fna/cds.fna -a GCF_005217605.1_ASM521760v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:35,754] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:35,755] [INFO] Task started: HMMsearch
[2024-01-24 13:25:35,755] [INFO] Running command: hmmsearch --tblout GCF_005217605.1_ASM521760v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a72cf8d-9cc3-4b06-9855-990be917cf75/dqc_reference/reference_markers.hmm GCF_005217605.1_ASM521760v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:35,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:35,997] [INFO] Found 6/6 markers.
[2024-01-24 13:25:36,024] [INFO] Query marker FASTA was written to GCF_005217605.1_ASM521760v1_genomic.fna/markers.fasta
[2024-01-24 13:25:36,025] [INFO] Task started: Blastn
[2024-01-24 13:25:36,025] [INFO] Running command: blastn -query GCF_005217605.1_ASM521760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a72cf8d-9cc3-4b06-9855-990be917cf75/dqc_reference/reference_markers.fasta -out GCF_005217605.1_ASM521760v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:36,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:36,646] [INFO] Selected 9 target genomes.
[2024-01-24 13:25:36,646] [INFO] Target genome list was writen to GCF_005217605.1_ASM521760v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:36,664] [INFO] Task started: fastANI
[2024-01-24 13:25:36,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg230e902d-372e-497c-b9f3-4ed9743506db/GCF_005217605.1_ASM521760v1_genomic.fna.gz --refList GCF_005217605.1_ASM521760v1_genomic.fna/target_genomes.txt --output GCF_005217605.1_ASM521760v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:40,683] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:40,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a72cf8d-9cc3-4b06-9855-990be917cf75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:40,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a72cf8d-9cc3-4b06-9855-990be917cf75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:40,691] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:40,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:40,692] [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
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	100.0	732	732	95	conclusive
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	80.9908	350	732	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	79.0211	263	732	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	78.287	105	732	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	78.243	205	732	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.0089	193	732	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	77.8291	163	732	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.7116	168	732	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.2993	128	732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:40,693] [INFO] DFAST Taxonomy check result was written to GCF_005217605.1_ASM521760v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:40,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:40,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:40,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a72cf8d-9cc3-4b06-9855-990be917cf75/dqc_reference/checkm_data
[2024-01-24 13:25:40,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:40,722] [INFO] Task started: CheckM
[2024-01-24 13:25:40,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005217605.1_ASM521760v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005217605.1_ASM521760v1_genomic.fna/checkm_input GCF_005217605.1_ASM521760v1_genomic.fna/checkm_result
[2024-01-24 13:26:02,125] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:02,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:02,148] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:02,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:02,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005217605.1_ASM521760v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:02,150] [INFO] Task started: Blastn
[2024-01-24 13:26:02,150] [INFO] Running command: blastn -query GCF_005217605.1_ASM521760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a72cf8d-9cc3-4b06-9855-990be917cf75/dqc_reference/reference_markers_gtdb.fasta -out GCF_005217605.1_ASM521760v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:02,981] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:02,985] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:02,986] [INFO] Target genome list was writen to GCF_005217605.1_ASM521760v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:03,018] [INFO] Task started: fastANI
[2024-01-24 13:26:03,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg230e902d-372e-497c-b9f3-4ed9743506db/GCF_005217605.1_ASM521760v1_genomic.fna.gz --refList GCF_005217605.1_ASM521760v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005217605.1_ASM521760v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:07,539] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:07,549] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:07,549] [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_005217605.1	s__Sulfurimonas crateris	100.0	732	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014859695.1	s__Sulfurimonas sp014859695	85.5353	522	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002899765.1	s__Sulfurimonas sp002899765	82.2827	462	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009883775.1	s__Sulfurimonas sp002452895	81.1003	353	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	-
GCA_001829675.1	s__Sulfurimonas sp001829675	79.372	344	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.77	99.75	0.96	0.96	4	-
GCA_001829715.1	s__Sulfurimonas sp001829715	79.2736	330	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
GCA_903903705.1	s__Sulfurimonas sp903903705	79.0732	186	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829785.1	s__Sulfurimonas sp001829785	79.0027	334	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.93	99.89	1.00	1.00	4	-
GCF_017357825.1	s__Sulfurimonas sp017357825	77.4694	99	732	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:07,551] [INFO] GTDB search result was written to GCF_005217605.1_ASM521760v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:07,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:07,556] [INFO] DFAST_QC result json was written to GCF_005217605.1_ASM521760v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:07,556] [INFO] DFAST_QC completed!
[2024-01-24 13:26:07,556] [INFO] Total running time: 0h0m38s