[2024-01-25 18:56:20,644] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:20,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:20,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg1471ffc9-1b1b-46ec-a85b-09195c1f3796/dqc_reference
[2024-01-25 18:56:21,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:21,774] [INFO] Task started: Prodigal
[2024-01-25 18:56:21,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg10680082-9bee-4d88-8eec-a2c38bf16fff/GCF_009833085.1_ASM983308v1_genomic.fna.gz | prodigal -d GCF_009833085.1_ASM983308v1_genomic.fna/cds.fna -a GCF_009833085.1_ASM983308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:29,594] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:29,595] [INFO] Task started: HMMsearch
[2024-01-25 18:56:29,595] [INFO] Running command: hmmsearch --tblout GCF_009833085.1_ASM983308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1471ffc9-1b1b-46ec-a85b-09195c1f3796/dqc_reference/reference_markers.hmm GCF_009833085.1_ASM983308v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:29,800] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:29,801] [INFO] Found 6/6 markers.
[2024-01-25 18:56:29,825] [INFO] Query marker FASTA was written to GCF_009833085.1_ASM983308v1_genomic.fna/markers.fasta
[2024-01-25 18:56:29,825] [INFO] Task started: Blastn
[2024-01-25 18:56:29,825] [INFO] Running command: blastn -query GCF_009833085.1_ASM983308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1471ffc9-1b1b-46ec-a85b-09195c1f3796/dqc_reference/reference_markers.fasta -out GCF_009833085.1_ASM983308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:30,398] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:30,401] [INFO] Selected 19 target genomes.
[2024-01-25 18:56:30,401] [INFO] Target genome list was writen to GCF_009833085.1_ASM983308v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:30,407] [INFO] Task started: fastANI
[2024-01-25 18:56:30,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg10680082-9bee-4d88-8eec-a2c38bf16fff/GCF_009833085.1_ASM983308v1_genomic.fna.gz --refList GCF_009833085.1_ASM983308v1_genomic.fna/target_genomes.txt --output GCF_009833085.1_ASM983308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:42,079] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:42,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1471ffc9-1b1b-46ec-a85b-09195c1f3796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:42,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1471ffc9-1b1b-46ec-a85b-09195c1f3796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:42,085] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:42,086] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:42,086] [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
Nitrosomonas oligotropha	strain=Nm45	GCA_009833085.1	42354	42354	type	True	100.0	1006	1010	95	conclusive
Nitrosomonas ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	78.1452	277	1010	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	78.0799	278	1010	95	below_threshold
Nitrosomonas supralitoralis	strain=APG5	GCA_003011925.2	2116706	2116706	type	True	77.6355	252	1010	95	below_threshold
Nitrosospira lacus	strain=APG3	GCA_000355765.4	1288494	1288494	type	True	76.6876	67	1010	95	below_threshold
Nitrosomonas europaea	strain=ATCC 25978	GCA_900167395.1	915	915	type	True	76.6575	57	1010	95	below_threshold
Nitrosospira briensis	strain=C-128	GCA_000619905.2	35799	35799	reftype	True	76.2108	57	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:42,087] [INFO] DFAST Taxonomy check result was written to GCF_009833085.1_ASM983308v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:42,088] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:42,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:42,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1471ffc9-1b1b-46ec-a85b-09195c1f3796/dqc_reference/checkm_data
[2024-01-25 18:56:42,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:42,119] [INFO] Task started: CheckM
[2024-01-25 18:56:42,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009833085.1_ASM983308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009833085.1_ASM983308v1_genomic.fna/checkm_input GCF_009833085.1_ASM983308v1_genomic.fna/checkm_result
[2024-01-25 18:57:08,845] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:08,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:08,872] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:08,872] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:08,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009833085.1_ASM983308v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:08,873] [INFO] Task started: Blastn
[2024-01-25 18:57:08,873] [INFO] Running command: blastn -query GCF_009833085.1_ASM983308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1471ffc9-1b1b-46ec-a85b-09195c1f3796/dqc_reference/reference_markers_gtdb.fasta -out GCF_009833085.1_ASM983308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:09,770] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:09,773] [INFO] Selected 7 target genomes.
[2024-01-25 18:57:09,773] [INFO] Target genome list was writen to GCF_009833085.1_ASM983308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:09,783] [INFO] Task started: fastANI
[2024-01-25 18:57:09,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg10680082-9bee-4d88-8eec-a2c38bf16fff/GCF_009833085.1_ASM983308v1_genomic.fna.gz --refList GCF_009833085.1_ASM983308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009833085.1_ASM983308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:15,144] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:15,150] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:15,150] [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_009833085.1	s__Nitrosomonas oligotropha	100.0	1006	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.57	96.57	0.86	0.86	2	conclusive
GCF_004345375.1	s__Nitrosomonas sp004345375	93.2396	857	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083595.1	s__Nitrosomonas sp002083595	90.5716	728	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106555.1	s__Nitrosomonas oligotropha_A	90.0222	809	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.13	95.07	0.88	0.80	7	-
GCA_015709635.1	s__Nitrosomonas sp015709635	82.7574	698	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	95.39	95.39	0.89	0.89	2	-
GCA_015709615.1	s__Nitrosomonas sp015709615	81.9554	710	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.12	98.12	0.95	0.95	2	-
GCA_018240285.1	s__Nitrosomonas sp018240285	81.7928	656	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	97.27	97.27	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:15,151] [INFO] GTDB search result was written to GCF_009833085.1_ASM983308v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:15,152] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:15,154] [INFO] DFAST_QC result json was written to GCF_009833085.1_ASM983308v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:15,154] [INFO] DFAST_QC completed!
[2024-01-25 18:57:15,154] [INFO] Total running time: 0h0m55s