[2023-06-18 20:56:23,956] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:23,959] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:23,959] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb10bd6a-73f5-4ab9-b244-79263683a748/dqc_reference
[2023-06-18 20:56:25,248] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:25,249] [INFO] Task started: Prodigal
[2023-06-18 20:56:25,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg161f3f90-94bd-4d15-91f5-424a2b8c6f27/GCA_018655135.1_ASM1865513v1_genomic.fna.gz | prodigal -d GCA_018655135.1_ASM1865513v1_genomic.fna/cds.fna -a GCA_018655135.1_ASM1865513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:26,358] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:26,358] [INFO] Task started: HMMsearch
[2023-06-18 20:56:26,358] [INFO] Running command: hmmsearch --tblout GCA_018655135.1_ASM1865513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb10bd6a-73f5-4ab9-b244-79263683a748/dqc_reference/reference_markers.hmm GCA_018655135.1_ASM1865513v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:26,517] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:26,518] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg161f3f90-94bd-4d15-91f5-424a2b8c6f27/GCA_018655135.1_ASM1865513v1_genomic.fna.gz]
[2023-06-18 20:56:26,536] [INFO] Query marker FASTA was written to GCA_018655135.1_ASM1865513v1_genomic.fna/markers.fasta
[2023-06-18 20:56:26,536] [INFO] Task started: Blastn
[2023-06-18 20:56:26,536] [INFO] Running command: blastn -query GCA_018655135.1_ASM1865513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb10bd6a-73f5-4ab9-b244-79263683a748/dqc_reference/reference_markers.fasta -out GCA_018655135.1_ASM1865513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:27,957] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:27,962] [INFO] Selected 4 target genomes.
[2023-06-18 20:56:27,963] [INFO] Target genome list was writen to GCA_018655135.1_ASM1865513v1_genomic.fna/target_genomes.txt
[2023-06-18 20:56:27,965] [INFO] Task started: fastANI
[2023-06-18 20:56:27,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg161f3f90-94bd-4d15-91f5-424a2b8c6f27/GCA_018655135.1_ASM1865513v1_genomic.fna.gz --refList GCA_018655135.1_ASM1865513v1_genomic.fna/target_genomes.txt --output GCA_018655135.1_ASM1865513v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:56:29,122] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:29,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb10bd6a-73f5-4ab9-b244-79263683a748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:56:29,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb10bd6a-73f5-4ab9-b244-79263683a748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:56:29,133] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:56:29,133] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:56:29,133] [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
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.8368	118	152	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	81.5537	125	152	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	80.9401	117	152	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	80.7475	121	152	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:56:29,135] [INFO] DFAST Taxonomy check result was written to GCA_018655135.1_ASM1865513v1_genomic.fna/tc_result.tsv
[2023-06-18 20:56:29,135] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:56:29,135] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:56:29,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb10bd6a-73f5-4ab9-b244-79263683a748/dqc_reference/checkm_data
[2023-06-18 20:56:29,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:56:29,148] [INFO] Task started: CheckM
[2023-06-18 20:56:29,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018655135.1_ASM1865513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018655135.1_ASM1865513v1_genomic.fna/checkm_input GCA_018655135.1_ASM1865513v1_genomic.fna/checkm_result
[2023-06-18 20:56:43,341] [INFO] Task succeeded: CheckM
[2023-06-18 20:56:43,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.36%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:56:43,377] [INFO] ===== Completeness check finished =====
[2023-06-18 20:56:43,378] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:56:43,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018655135.1_ASM1865513v1_genomic.fna/markers.fasta)
[2023-06-18 20:56:43,379] [INFO] Task started: Blastn
[2023-06-18 20:56:43,379] [INFO] Running command: blastn -query GCA_018655135.1_ASM1865513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb10bd6a-73f5-4ab9-b244-79263683a748/dqc_reference/reference_markers_gtdb.fasta -out GCA_018655135.1_ASM1865513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:43,843] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:43,847] [INFO] Selected 5 target genomes.
[2023-06-18 20:56:43,847] [INFO] Target genome list was writen to GCA_018655135.1_ASM1865513v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:56:43,851] [INFO] Task started: fastANI
[2023-06-18 20:56:43,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg161f3f90-94bd-4d15-91f5-424a2b8c6f27/GCA_018655135.1_ASM1865513v1_genomic.fna.gz --refList GCA_018655135.1_ASM1865513v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018655135.1_ASM1865513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:56:44,724] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:44,733] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:56:44,733] [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
GCA_018674605.1	s__Nitrosopumilus sp018674605	99.1118	121	152	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.83	98.50	0.79	0.69	12	conclusive
GCA_905616385.1	s__Nitrosopumilus sp905616385	87.788	85	152	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	97.32	96.75	0.55	0.53	3	-
GCA_902514095.1	s__Nitrosopumilus sp902514095	87.2034	99	152	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001437625.1	s__Nitrosopumilus sp001437625	86.9782	122	152	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.62	95.42	0.85	0.75	5	-
GCA_905612295.1	s__Nitrosopumilus sp905612295	86.7095	88	152	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:56:44,735] [INFO] GTDB search result was written to GCA_018655135.1_ASM1865513v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:56:44,736] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:56:44,738] [INFO] DFAST_QC result json was written to GCA_018655135.1_ASM1865513v1_genomic.fna/dqc_result.json
[2023-06-18 20:56:44,739] [INFO] DFAST_QC completed!
[2023-06-18 20:56:44,739] [INFO] Total running time: 0h0m21s