[2024-01-24 13:52:12,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,343] [INFO] DQC Reference Directory: /var/lib/cwl/stgecf3bca0-7d05-4574-b4cb-535b68b11e4c/dqc_reference
[2024-01-24 13:52:13,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,542] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,542] [INFO] Running command: gunzip -c /var/lib/cwl/stge549ad87-01fe-49a5-ac5b-3b31a082d202/GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/cds.fna -a GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:17,989] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:17,989] [INFO] Task started: HMMsearch
[2024-01-24 13:52:17,989] [INFO] Running command: hmmsearch --tblout GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecf3bca0-7d05-4574-b4cb-535b68b11e4c/dqc_reference/reference_markers.hmm GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:18,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:18,230] [INFO] Found 6/6 markers.
[2024-01-24 13:52:18,257] [INFO] Query marker FASTA was written to GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:52:18,258] [INFO] Task started: Blastn
[2024-01-24 13:52:18,258] [INFO] Running command: blastn -query GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgecf3bca0-7d05-4574-b4cb-535b68b11e4c/dqc_reference/reference_markers.fasta -out GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:18,869] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:18,873] [INFO] Selected 21 target genomes.
[2024-01-24 13:52:18,874] [INFO] Target genome list was writen to GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:52:18,892] [INFO] Task started: fastANI
[2024-01-24 13:52:18,893] [INFO] Running command: fastANI --query /var/lib/cwl/stge549ad87-01fe-49a5-ac5b-3b31a082d202/GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna.gz --refList GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:24,919] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:24,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecf3bca0-7d05-4574-b4cb-535b68b11e4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:24,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecf3bca0-7d05-4574-b4cb-535b68b11e4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:24,927] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:52:24,927] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:24,927] [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
Nitratiruptor tergarcus	strain=DSM 16512	GCA_900176045.1	269259	269259	type	True	100.0	640	642	95	conclusive
Nitrosophilus labii	strain=HRV44	GCA_014466985.1	2706014	2706014	type	True	77.2111	101	642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:24,930] [INFO] DFAST Taxonomy check result was written to GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:52:24,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:24,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:24,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecf3bca0-7d05-4574-b4cb-535b68b11e4c/dqc_reference/checkm_data
[2024-01-24 13:52:24,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:24,957] [INFO] Task started: CheckM
[2024-01-24 13:52:24,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/checkm_input GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:52:45,442] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:45,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:45,464] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:45,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:45,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:52:45,466] [INFO] Task started: Blastn
[2024-01-24 13:52:45,466] [INFO] Running command: blastn -query GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgecf3bca0-7d05-4574-b4cb-535b68b11e4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:46,245] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:46,250] [INFO] Selected 18 target genomes.
[2024-01-24 13:52:46,250] [INFO] Target genome list was writen to GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:46,277] [INFO] Task started: fastANI
[2024-01-24 13:52:46,278] [INFO] Running command: fastANI --query /var/lib/cwl/stge549ad87-01fe-49a5-ac5b-3b31a082d202/GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna.gz --refList GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:52,706] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:52,717] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:52,717] [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_900176045.1	s__Nitratiruptor tergarcus	100.0	639	642	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	95.63	95.63	0.89	0.89	3	conclusive
GCF_016593235.1	s__Nitratiruptor sp016593235	81.0982	279	642	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629565.1	s__YY08-10 sp016629565	80.3643	200	642	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__YY08-10	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000010325.1	s__YY08-10 sp000010325	79.9097	209	642	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__YY08-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494535.1	s__Nitratiruptor sp015494535	77.9498	136	642	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494595.1	s__Nitratiruptor sp015494595	77.8054	151	642	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:52,719] [INFO] GTDB search result was written to GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:52,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:52,722] [INFO] DFAST_QC result json was written to GCF_900176045.1_IMG-taxon_2516493030_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:52:52,722] [INFO] DFAST_QC completed!
[2024-01-24 13:52:52,722] [INFO] Total running time: 0h0m40s