[2024-01-24 13:37:05,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg293cd314-c1cf-469a-8d72-e67f6609f41e/dqc_reference
[2024-01-24 13:37:06,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,418] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,418] [INFO] Running command: gunzip -c /var/lib/cwl/stgc23b776f-332b-483a-a722-340f77223e21/GCF_000143085.1_ASM14308v1_genomic.fna.gz | prodigal -d GCF_000143085.1_ASM14308v1_genomic.fna/cds.fna -a GCF_000143085.1_ASM14308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:15,292] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:15,293] [INFO] Task started: HMMsearch
[2024-01-24 13:37:15,293] [INFO] Running command: hmmsearch --tblout GCF_000143085.1_ASM14308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg293cd314-c1cf-469a-8d72-e67f6609f41e/dqc_reference/reference_markers.hmm GCF_000143085.1_ASM14308v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:15,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:15,622] [INFO] Found 6/6 markers.
[2024-01-24 13:37:15,653] [INFO] Query marker FASTA was written to GCF_000143085.1_ASM14308v1_genomic.fna/markers.fasta
[2024-01-24 13:37:15,653] [INFO] Task started: Blastn
[2024-01-24 13:37:15,653] [INFO] Running command: blastn -query GCF_000143085.1_ASM14308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293cd314-c1cf-469a-8d72-e67f6609f41e/dqc_reference/reference_markers.fasta -out GCF_000143085.1_ASM14308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:16,309] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:16,312] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:16,313] [INFO] Target genome list was writen to GCF_000143085.1_ASM14308v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:16,318] [INFO] Task started: fastANI
[2024-01-24 13:37:16,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgc23b776f-332b-483a-a722-340f77223e21/GCF_000143085.1_ASM14308v1_genomic.fna.gz --refList GCF_000143085.1_ASM14308v1_genomic.fna/target_genomes.txt --output GCF_000143085.1_ASM14308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:25,936] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:25,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg293cd314-c1cf-469a-8d72-e67f6609f41e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:25,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg293cd314-c1cf-469a-8d72-e67f6609f41e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:25,943] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:25,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:25,943] [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 watsonii	strain=C-113	GCA_000143085.1	473531	473531	type	True	100.0	1120	1123	95	conclusive
Nitrosococcus oceani	strain=ATCC 19707	GCA_000012805.1	1229	1229	type	True	89.3301	953	1123	95	below_threshold
Nitrosococcus wardiae	strain=D1FHS	GCA_004421105.1	1814290	1814290	type	True	78.2397	406	1123	95	below_threshold
Nitrosococcus halophilus	strain=Nc 4	GCA_000024725.1	133539	133539	type	True	78.2236	459	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:25,945] [INFO] DFAST Taxonomy check result was written to GCF_000143085.1_ASM14308v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:25,946] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:25,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:25,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg293cd314-c1cf-469a-8d72-e67f6609f41e/dqc_reference/checkm_data
[2024-01-24 13:37:25,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:25,990] [INFO] Task started: CheckM
[2024-01-24 13:37:25,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000143085.1_ASM14308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000143085.1_ASM14308v1_genomic.fna/checkm_input GCF_000143085.1_ASM14308v1_genomic.fna/checkm_result
[2024-01-24 13:37:59,683] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:59,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:59,722] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:59,722] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:59,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000143085.1_ASM14308v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:59,723] [INFO] Task started: Blastn
[2024-01-24 13:37:59,723] [INFO] Running command: blastn -query GCF_000143085.1_ASM14308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293cd314-c1cf-469a-8d72-e67f6609f41e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000143085.1_ASM14308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:00,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:00,803] [INFO] Selected 13 target genomes.
[2024-01-24 13:38:00,803] [INFO] Target genome list was writen to GCF_000143085.1_ASM14308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:00,831] [INFO] Task started: fastANI
[2024-01-24 13:38:00,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgc23b776f-332b-483a-a722-340f77223e21/GCF_000143085.1_ASM14308v1_genomic.fna.gz --refList GCF_000143085.1_ASM14308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000143085.1_ASM14308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:11,686] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:11,695] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:11,696] [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_000143085.1	s__Nitrosococcus watsonii	100.0	1119	1123	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_000012805.1	s__Nitrosococcus oceani	89.3179	955	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Nitrosococcaceae;g__Nitrosococcus	95.0	99.51	98.08	0.98	0.93	5	-
GCF_004421105.1	s__Nitrosococcus wardiae	78.2587	408	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Nitrosococcaceae;g__Nitrosococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024725.1	s__Nitrosococcus halophilus	78.2475	461	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Nitrosococcaceae;g__Nitrosococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356115.1	s__Nitrosoglobus terrae	77.2425	71	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Nitrosococcaceae;g__Nitrosoglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:11,697] [INFO] GTDB search result was written to GCF_000143085.1_ASM14308v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:11,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:11,701] [INFO] DFAST_QC result json was written to GCF_000143085.1_ASM14308v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:11,701] [INFO] DFAST_QC completed!
[2024-01-24 13:38:11,701] [INFO] Total running time: 0h1m7s