[2023-03-19 04:55:39,480] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:55:39,481] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:55:39,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg963c95a3-b875-4109-8d28-6ec31839a2de/dqc_reference
[2023-03-19 04:55:40,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:55:40,591] [INFO] Task started: Prodigal
[2023-03-19 04:55:40,591] [INFO] Running command: cat /var/lib/cwl/stg0ee5a630-104c-4829-be55-77af2fee42c6/OceanDNA-a735.fa | prodigal -d OceanDNA-a735/cds.fna -a OceanDNA-a735/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:55:49,879] [INFO] Task succeeded: Prodigal
[2023-03-19 04:55:49,879] [INFO] Task started: HMMsearch
[2023-03-19 04:55:49,879] [INFO] Running command: hmmsearch --tblout OceanDNA-a735/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg963c95a3-b875-4109-8d28-6ec31839a2de/dqc_reference/reference_markers.hmm OceanDNA-a735/protein.faa > /dev/null
[2023-03-19 04:55:49,998] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:55:49,998] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0ee5a630-104c-4829-be55-77af2fee42c6/OceanDNA-a735.fa]
[2023-03-19 04:55:50,017] [INFO] Query marker FASTA was written to OceanDNA-a735/markers.fasta
[2023-03-19 04:55:50,018] [INFO] Task started: Blastn
[2023-03-19 04:55:50,018] [INFO] Running command: blastn -query OceanDNA-a735/markers.fasta -db /var/lib/cwl/stg963c95a3-b875-4109-8d28-6ec31839a2de/dqc_reference/reference_markers.fasta -out OceanDNA-a735/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:55:50,448] [INFO] Task succeeded: Blastn
[2023-03-19 04:55:50,452] [INFO] Selected 4 target genomes.
[2023-03-19 04:55:50,452] [INFO] Target genome list was writen to OceanDNA-a735/target_genomes.txt
[2023-03-19 04:55:50,455] [INFO] Task started: fastANI
[2023-03-19 04:55:50,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee5a630-104c-4829-be55-77af2fee42c6/OceanDNA-a735.fa --refList OceanDNA-a735/target_genomes.txt --output OceanDNA-a735/fastani_result.tsv --threads 1
[2023-03-19 04:55:51,948] [INFO] Task succeeded: fastANI
[2023-03-19 04:55:51,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg963c95a3-b875-4109-8d28-6ec31839a2de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:55:51,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg963c95a3-b875-4109-8d28-6ec31839a2de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:55:51,953] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:55:51,953] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:55:51,953] [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	82.0489	321	472	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.9645	316	472	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.7727	329	472	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	80.8666	306	472	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:55:51,955] [INFO] DFAST Taxonomy check result was written to OceanDNA-a735/tc_result.tsv
[2023-03-19 04:55:51,957] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:55:51,957] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:55:51,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg963c95a3-b875-4109-8d28-6ec31839a2de/dqc_reference/checkm_data
[2023-03-19 04:55:51,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:55:51,962] [INFO] Task started: CheckM
[2023-03-19 04:55:51,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a735/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a735/checkm_input OceanDNA-a735/checkm_result
[2023-03-19 04:56:17,659] [INFO] Task succeeded: CheckM
[2023-03-19 04:56:17,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:56:17,672] [INFO] ===== Completeness check finished =====
[2023-03-19 04:56:17,673] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:56:17,673] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a735/markers.fasta)
[2023-03-19 04:56:17,674] [INFO] Task started: Blastn
[2023-03-19 04:56:17,674] [INFO] Running command: blastn -query OceanDNA-a735/markers.fasta -db /var/lib/cwl/stg963c95a3-b875-4109-8d28-6ec31839a2de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a735/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:56:18,106] [INFO] Task succeeded: Blastn
[2023-03-19 04:56:18,107] [INFO] Selected 7 target genomes.
[2023-03-19 04:56:18,107] [INFO] Target genome list was writen to OceanDNA-a735/target_genomes_gtdb.txt
[2023-03-19 04:56:18,114] [INFO] Task started: fastANI
[2023-03-19 04:56:18,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee5a630-104c-4829-be55-77af2fee42c6/OceanDNA-a735.fa --refList OceanDNA-a735/target_genomes_gtdb.txt --output OceanDNA-a735/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:56:20,504] [INFO] Task succeeded: fastANI
[2023-03-19 04:56:20,508] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:56:20,509] [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_013215285.1	s__Nitrosopumilus sp013215285	99.9751	467	472	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013911135.1	s__Nitrosopumilus sp013911135	84.1541	322	472	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	84.0061	312	472	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002317795.1	s__Nitrosopumilus sp002317795	83.0696	326	472	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018668425.1	s__Nitrosopumilus sp018668425	82.471	267	472	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.76	99.71	0.87	0.86	3	-
GCA_014384555.1	s__Nitrosopumilus sp014384555	82.098	294	472	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.46	99.38	0.88	0.87	3	-
GCA_005798405.1	s__Nitrosarchaeum sp005798405	79.2564	222	472	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	99.84	99.81	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2023-03-19 04:56:20,509] [INFO] GTDB search result was written to OceanDNA-a735/result_gtdb.tsv
[2023-03-19 04:56:20,510] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:56:20,512] [INFO] DFAST_QC result json was written to OceanDNA-a735/dqc_result.json
[2023-03-19 04:56:20,512] [INFO] DFAST_QC completed!
[2023-03-19 04:56:20,512] [INFO] Total running time: 0h0m41s