[2023-03-18 01:26:26,319] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,320] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,320] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb211a00-57a9-485d-b1c4-a5e08ba64723/dqc_reference
[2023-03-18 01:26:27,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,484] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,484] [INFO] Running command: cat /var/lib/cwl/stg2963757d-55ed-445c-8dc5-61bf8fe4c448/OceanDNA-a485.fa | prodigal -d OceanDNA-a485/cds.fna -a OceanDNA-a485/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:32,633] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:32,634] [INFO] Task started: HMMsearch
[2023-03-18 01:26:32,634] [INFO] Running command: hmmsearch --tblout OceanDNA-a485/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb211a00-57a9-485d-b1c4-a5e08ba64723/dqc_reference/reference_markers.hmm OceanDNA-a485/protein.faa > /dev/null
[2023-03-18 01:26:32,757] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:32,758] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg2963757d-55ed-445c-8dc5-61bf8fe4c448/OceanDNA-a485.fa]
[2023-03-18 01:26:32,766] [INFO] Query marker FASTA was written to OceanDNA-a485/markers.fasta
[2023-03-18 01:26:32,767] [INFO] Task started: Blastn
[2023-03-18 01:26:32,767] [INFO] Running command: blastn -query OceanDNA-a485/markers.fasta -db /var/lib/cwl/stgcb211a00-57a9-485d-b1c4-a5e08ba64723/dqc_reference/reference_markers.fasta -out OceanDNA-a485/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:33,200] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:33,201] [INFO] Selected 3 target genomes.
[2023-03-18 01:26:33,201] [INFO] Target genome list was writen to OceanDNA-a485/target_genomes.txt
[2023-03-18 01:26:33,204] [INFO] Task started: fastANI
[2023-03-18 01:26:33,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg2963757d-55ed-445c-8dc5-61bf8fe4c448/OceanDNA-a485.fa --refList OceanDNA-a485/target_genomes.txt --output OceanDNA-a485/fastani_result.tsv --threads 1
[2023-03-18 01:26:34,289] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:34,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb211a00-57a9-485d-b1c4-a5e08ba64723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:34,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb211a00-57a9-485d-b1c4-a5e08ba64723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:34,307] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:34,307] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:26:34,307] [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	83.5806	248	282	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	82.3956	237	282	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	80.6424	201	282	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:26:34,307] [INFO] DFAST Taxonomy check result was written to OceanDNA-a485/tc_result.tsv
[2023-03-18 01:26:34,307] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:34,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:34,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb211a00-57a9-485d-b1c4-a5e08ba64723/dqc_reference/checkm_data
[2023-03-18 01:26:34,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:34,311] [INFO] Task started: CheckM
[2023-03-18 01:26:34,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a485/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a485/checkm_input OceanDNA-a485/checkm_result
[2023-03-18 01:26:54,588] [INFO] Task succeeded: CheckM
[2023-03-18 01:26:54,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:26:54,591] [INFO] ===== Completeness check finished =====
[2023-03-18 01:26:54,591] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:26:54,591] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a485/markers.fasta)
[2023-03-18 01:26:54,592] [INFO] Task started: Blastn
[2023-03-18 01:26:54,592] [INFO] Running command: blastn -query OceanDNA-a485/markers.fasta -db /var/lib/cwl/stgcb211a00-57a9-485d-b1c4-a5e08ba64723/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a485/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:55,235] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:55,235] [INFO] Selected 5 target genomes.
[2023-03-18 01:26:55,235] [INFO] Target genome list was writen to OceanDNA-a485/target_genomes_gtdb.txt
[2023-03-18 01:26:55,247] [INFO] Task started: fastANI
[2023-03-18 01:26:55,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg2963757d-55ed-445c-8dc5-61bf8fe4c448/OceanDNA-a485.fa --refList OceanDNA-a485/target_genomes_gtdb.txt --output OceanDNA-a485/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:26:56,826] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:56,830] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:26:56,830] [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_013203245.1	s__Nitrosopumilus sp013203245	89.6261	207	282	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479565.1	s__Nitrosopumilus sp905479565	83.0101	216	282	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407145.1	s__Nitrosopumilus cobalaminigenes	82.3956	237	282	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510275.1	s__Nitrosopumilus sp001510275	80.3838	187	282	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014078525.1	s__Nitrosopumilus sp014078525	79.9576	189	282	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:26:56,831] [INFO] GTDB search result was written to OceanDNA-a485/result_gtdb.tsv
[2023-03-18 01:26:56,831] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:26:56,832] [INFO] DFAST_QC result json was written to OceanDNA-a485/dqc_result.json
[2023-03-18 01:26:56,832] [INFO] DFAST_QC completed!
[2023-03-18 01:26:56,832] [INFO] Total running time: 0h0m31s