[2023-06-19 02:25:29,360] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:25:29,362] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:25:29,363] [INFO] DQC Reference Directory: /var/lib/cwl/stgf809ae42-1391-4b22-b612-2bae83e25884/dqc_reference
[2023-06-19 02:25:30,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:25:30,582] [INFO] Task started: Prodigal
[2023-06-19 02:25:30,582] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c450676-cedd-495e-a267-f426dbde47c1/GCA_013043885.1_ASM1304388v1_genomic.fna.gz | prodigal -d GCA_013043885.1_ASM1304388v1_genomic.fna/cds.fna -a GCA_013043885.1_ASM1304388v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:25:32,062] [INFO] Task succeeded: Prodigal
[2023-06-19 02:25:32,063] [INFO] Task started: HMMsearch
[2023-06-19 02:25:32,063] [INFO] Running command: hmmsearch --tblout GCA_013043885.1_ASM1304388v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf809ae42-1391-4b22-b612-2bae83e25884/dqc_reference/reference_markers.hmm GCA_013043885.1_ASM1304388v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:25:32,181] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:25:32,182] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6c450676-cedd-495e-a267-f426dbde47c1/GCA_013043885.1_ASM1304388v1_genomic.fna.gz]
[2023-06-19 02:25:32,207] [INFO] Query marker FASTA was written to GCA_013043885.1_ASM1304388v1_genomic.fna/markers.fasta
[2023-06-19 02:25:32,207] [INFO] Task started: Blastn
[2023-06-19 02:25:32,207] [INFO] Running command: blastn -query GCA_013043885.1_ASM1304388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf809ae42-1391-4b22-b612-2bae83e25884/dqc_reference/reference_markers.fasta -out GCA_013043885.1_ASM1304388v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:33,688] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:33,704] [INFO] Selected 5 target genomes.
[2023-06-19 02:25:33,705] [INFO] Target genome list was writen to GCA_013043885.1_ASM1304388v1_genomic.fna/target_genomes.txt
[2023-06-19 02:25:33,706] [INFO] Task started: fastANI
[2023-06-19 02:25:33,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c450676-cedd-495e-a267-f426dbde47c1/GCA_013043885.1_ASM1304388v1_genomic.fna.gz --refList GCA_013043885.1_ASM1304388v1_genomic.fna/target_genomes.txt --output GCA_013043885.1_ASM1304388v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:25:35,453] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:35,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf809ae42-1391-4b22-b612-2bae83e25884/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:25:35,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf809ae42-1391-4b22-b612-2bae83e25884/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:25:35,459] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:25:35,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:25:35,460] [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 cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	84.6949	187	227	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	84.1501	181	227	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	82.964	174	227	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	82.6685	164	227	95	below_threshold
Nitrosopumilus maritimus	strain=SCM1	GCA_000018465.1	338192	338192	type	True	81.1569	157	227	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:25:35,461] [INFO] DFAST Taxonomy check result was written to GCA_013043885.1_ASM1304388v1_genomic.fna/tc_result.tsv
[2023-06-19 02:25:35,462] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:25:35,462] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:25:35,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf809ae42-1391-4b22-b612-2bae83e25884/dqc_reference/checkm_data
[2023-06-19 02:25:35,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:25:35,474] [INFO] Task started: CheckM
[2023-06-19 02:25:35,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013043885.1_ASM1304388v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013043885.1_ASM1304388v1_genomic.fna/checkm_input GCA_013043885.1_ASM1304388v1_genomic.fna/checkm_result
[2023-06-19 02:25:48,677] [INFO] Task succeeded: CheckM
[2023-06-19 02:25:48,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.92%
Contamintation: 10.42%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-19 02:25:48,697] [INFO] ===== Completeness check finished =====
[2023-06-19 02:25:48,697] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:25:48,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013043885.1_ASM1304388v1_genomic.fna/markers.fasta)
[2023-06-19 02:25:48,698] [INFO] Task started: Blastn
[2023-06-19 02:25:48,698] [INFO] Running command: blastn -query GCA_013043885.1_ASM1304388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf809ae42-1391-4b22-b612-2bae83e25884/dqc_reference/reference_markers_gtdb.fasta -out GCA_013043885.1_ASM1304388v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:49,170] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:49,174] [INFO] Selected 7 target genomes.
[2023-06-19 02:25:49,174] [INFO] Target genome list was writen to GCA_013043885.1_ASM1304388v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:25:49,177] [INFO] Task started: fastANI
[2023-06-19 02:25:49,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c450676-cedd-495e-a267-f426dbde47c1/GCA_013043885.1_ASM1304388v1_genomic.fna.gz --refList GCA_013043885.1_ASM1304388v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013043885.1_ASM1304388v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:25:51,192] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:51,200] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:25:51,200] [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_013043295.1	s__Nitrosopumilus sp013043295	97.568	167	227	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCF_013407145.1	s__Nitrosopumilus cobalaminigenes	84.6949	187	227	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384555.1	s__Nitrosopumilus sp014384555	83.7814	167	227	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.46	99.38	0.88	0.87	3	-
GCF_014078525.1	s__Nitrosopumilus sp014078525	83.7695	178	227	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299395.1	s__Nitrosopumilus sediminis	83.1666	182	227	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956175.1	s__Nitrosopumilus adriaticus	82.964	174	227	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215285.1	s__Nitrosopumilus sp013215285	81.404	160	227	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:25:51,209] [INFO] GTDB search result was written to GCA_013043885.1_ASM1304388v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:25:51,210] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:25:51,213] [INFO] DFAST_QC result json was written to GCA_013043885.1_ASM1304388v1_genomic.fna/dqc_result.json
[2023-06-19 02:25:51,213] [INFO] DFAST_QC completed!
[2023-06-19 02:25:51,213] [INFO] Total running time: 0h0m22s