[2024-01-25 18:06:20,599] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:20,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:20,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg5986e12b-faa2-4403-9ac5-d38219ca92dc/dqc_reference
[2024-01-25 18:06:21,748] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:21,749] [INFO] Task started: Prodigal
[2024-01-25 18:06:21,749] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e0afafb-8721-4fb0-8d87-e00f29f81d0b/GCF_000024725.1_ASM2472v1_genomic.fna.gz | prodigal -d GCF_000024725.1_ASM2472v1_genomic.fna/cds.fna -a GCF_000024725.1_ASM2472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:31,504] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:31,504] [INFO] Task started: HMMsearch
[2024-01-25 18:06:31,504] [INFO] Running command: hmmsearch --tblout GCF_000024725.1_ASM2472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5986e12b-faa2-4403-9ac5-d38219ca92dc/dqc_reference/reference_markers.hmm GCF_000024725.1_ASM2472v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:31,772] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:31,773] [INFO] Found 6/6 markers.
[2024-01-25 18:06:31,806] [INFO] Query marker FASTA was written to GCF_000024725.1_ASM2472v1_genomic.fna/markers.fasta
[2024-01-25 18:06:31,806] [INFO] Task started: Blastn
[2024-01-25 18:06:31,807] [INFO] Running command: blastn -query GCF_000024725.1_ASM2472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5986e12b-faa2-4403-9ac5-d38219ca92dc/dqc_reference/reference_markers.fasta -out GCF_000024725.1_ASM2472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:32,396] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:32,399] [INFO] Selected 13 target genomes.
[2024-01-25 18:06:32,400] [INFO] Target genome list was writen to GCF_000024725.1_ASM2472v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:32,410] [INFO] Task started: fastANI
[2024-01-25 18:06:32,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e0afafb-8721-4fb0-8d87-e00f29f81d0b/GCF_000024725.1_ASM2472v1_genomic.fna.gz --refList GCF_000024725.1_ASM2472v1_genomic.fna/target_genomes.txt --output GCF_000024725.1_ASM2472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:42,409] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:42,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5986e12b-faa2-4403-9ac5-d38219ca92dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:42,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5986e12b-faa2-4403-9ac5-d38219ca92dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:42,415] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:42,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:42,415] [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
Nitrosococcus halophilus	strain=Nc 4	GCA_000024725.1	133539	133539	type	True	100.0	1375	1380	95	conclusive
Nitrosococcus wardiae	strain=D1FHS	GCA_004421105.1	1814290	1814290	type	True	89.4241	1015	1380	95	below_threshold
Nitrosococcus oceani	strain=ATCC 19707	GCA_000012805.1	1229	1229	type	True	78.583	505	1380	95	below_threshold
Nitrosococcus watsonii	strain=C-113	GCA_000143085.1	473531	473531	type	True	78.3321	440	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:42,416] [INFO] DFAST Taxonomy check result was written to GCF_000024725.1_ASM2472v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:42,417] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:42,417] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:42,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5986e12b-faa2-4403-9ac5-d38219ca92dc/dqc_reference/checkm_data
[2024-01-25 18:06:42,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:42,456] [INFO] Task started: CheckM
[2024-01-25 18:06:42,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024725.1_ASM2472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024725.1_ASM2472v1_genomic.fna/checkm_input GCF_000024725.1_ASM2472v1_genomic.fna/checkm_result
[2024-01-25 18:07:13,400] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:13,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:13,420] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:13,420] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:13,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024725.1_ASM2472v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:13,421] [INFO] Task started: Blastn
[2024-01-25 18:07:13,421] [INFO] Running command: blastn -query GCF_000024725.1_ASM2472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5986e12b-faa2-4403-9ac5-d38219ca92dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024725.1_ASM2472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:14,422] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:14,424] [INFO] Selected 12 target genomes.
[2024-01-25 18:07:14,424] [INFO] Target genome list was writen to GCF_000024725.1_ASM2472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:14,433] [INFO] Task started: fastANI
[2024-01-25 18:07:14,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e0afafb-8721-4fb0-8d87-e00f29f81d0b/GCF_000024725.1_ASM2472v1_genomic.fna.gz --refList GCF_000024725.1_ASM2472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024725.1_ASM2472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:23,325] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:23,329] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:23,329] [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_000024725.1	s__Nitrosococcus halophilus	100.0	1375	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Nitrosococcaceae;g__Nitrosococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004421105.1	s__Nitrosococcus wardiae	89.4054	1017	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Nitrosococcaceae;g__Nitrosococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012805.1	s__Nitrosococcus oceani	78.5741	506	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Nitrosococcaceae;g__Nitrosococcus	95.0	99.51	98.08	0.98	0.93	5	-
GCF_000143085.1	s__Nitrosococcus watsonii	78.3167	439	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Nitrosococcaceae;g__Nitrosococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:23,331] [INFO] GTDB search result was written to GCF_000024725.1_ASM2472v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:23,331] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:23,333] [INFO] DFAST_QC result json was written to GCF_000024725.1_ASM2472v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:23,333] [INFO] DFAST_QC completed!
[2024-01-25 18:07:23,334] [INFO] Total running time: 0h1m3s