[2024-01-25 18:13:20,605] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,607] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb28a704-36b6-49b8-82f6-03ae9ca98893/dqc_reference
[2024-01-25 18:13:21,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,770] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,770] [INFO] Running command: gunzip -c /var/lib/cwl/stg71442029-598c-4f06-a5b0-9c03972078f2/GCF_014466985.1_ASM1446698v1_genomic.fna.gz | prodigal -d GCF_014466985.1_ASM1446698v1_genomic.fna/cds.fna -a GCF_014466985.1_ASM1446698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:25,138] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:25,138] [INFO] Task started: HMMsearch
[2024-01-25 18:13:25,138] [INFO] Running command: hmmsearch --tblout GCF_014466985.1_ASM1446698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb28a704-36b6-49b8-82f6-03ae9ca98893/dqc_reference/reference_markers.hmm GCF_014466985.1_ASM1446698v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:25,385] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:25,387] [INFO] Found 6/6 markers.
[2024-01-25 18:13:25,408] [INFO] Query marker FASTA was written to GCF_014466985.1_ASM1446698v1_genomic.fna/markers.fasta
[2024-01-25 18:13:25,409] [INFO] Task started: Blastn
[2024-01-25 18:13:25,409] [INFO] Running command: blastn -query GCF_014466985.1_ASM1446698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb28a704-36b6-49b8-82f6-03ae9ca98893/dqc_reference/reference_markers.fasta -out GCF_014466985.1_ASM1446698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:25,958] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:25,963] [INFO] Selected 18 target genomes.
[2024-01-25 18:13:25,963] [INFO] Target genome list was writen to GCF_014466985.1_ASM1446698v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:26,002] [INFO] Task started: fastANI
[2024-01-25 18:13:26,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg71442029-598c-4f06-a5b0-9c03972078f2/GCF_014466985.1_ASM1446698v1_genomic.fna.gz --refList GCF_014466985.1_ASM1446698v1_genomic.fna/target_genomes.txt --output GCF_014466985.1_ASM1446698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:34,301] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:34,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb28a704-36b6-49b8-82f6-03ae9ca98893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:34,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb28a704-36b6-49b8-82f6-03ae9ca98893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:34,306] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:34,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:34,307] [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
Nitrosophilus labii	strain=HRV44	GCA_014466985.1	2706014	2706014	type	True	100.0	693	697	95	conclusive
Nitratiruptor tergarcus	strain=DSM 16512	GCA_900176045.1	269259	269259	type	True	77.6444	94	697	95	below_threshold
Nitrosophilus alvini	strain=EPR55-1	GCA_015100395.1	2714855	2714855	type	True	77.4384	134	697	95	below_threshold
Caminibacter mediatlanticus	strain=TB-2	GCA_005843985.1	291048	291048	type	True	76.4539	67	697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:34,308] [INFO] DFAST Taxonomy check result was written to GCF_014466985.1_ASM1446698v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:34,308] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:34,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:34,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb28a704-36b6-49b8-82f6-03ae9ca98893/dqc_reference/checkm_data
[2024-01-25 18:13:34,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:34,332] [INFO] Task started: CheckM
[2024-01-25 18:13:34,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014466985.1_ASM1446698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014466985.1_ASM1446698v1_genomic.fna/checkm_input GCF_014466985.1_ASM1446698v1_genomic.fna/checkm_result
[2024-01-25 18:13:51,182] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:51,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:51,204] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:51,204] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:51,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014466985.1_ASM1446698v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:51,204] [INFO] Task started: Blastn
[2024-01-25 18:13:51,205] [INFO] Running command: blastn -query GCF_014466985.1_ASM1446698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb28a704-36b6-49b8-82f6-03ae9ca98893/dqc_reference/reference_markers_gtdb.fasta -out GCF_014466985.1_ASM1446698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:51,996] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:52,000] [INFO] Selected 22 target genomes.
[2024-01-25 18:13:52,000] [INFO] Target genome list was writen to GCF_014466985.1_ASM1446698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:52,024] [INFO] Task started: fastANI
[2024-01-25 18:13:52,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg71442029-598c-4f06-a5b0-9c03972078f2/GCF_014466985.1_ASM1446698v1_genomic.fna.gz --refList GCF_014466985.1_ASM1446698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014466985.1_ASM1446698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:00,800] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:00,806] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:00,806] [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_014466985.1	s__Nitrosophilus_A labii	100.0	695	697	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitrosophilus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900176045.1	s__Nitratiruptor tergarcus	77.6444	94	697	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	95.63	95.63	0.89	0.89	3	-
GCF_016593235.1	s__Nitratiruptor sp016593235	77.6375	67	697	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015100395.1	s__Nitrosophilus alvini	77.5594	135	697	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitrosophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005843985.1	s__Caminibacter mediatlanticus	76.6013	69	697	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Caminibacter	95.0	98.80	98.80	0.94	0.94	2	-
GCA_016744535.1	s__BB28 sp016744535	75.2524	58	697	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__BB28;g__BB28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:00,807] [INFO] GTDB search result was written to GCF_014466985.1_ASM1446698v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:00,808] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:00,811] [INFO] DFAST_QC result json was written to GCF_014466985.1_ASM1446698v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:00,811] [INFO] DFAST_QC completed!
[2024-01-25 18:14:00,811] [INFO] Total running time: 0h0m40s