[2023-03-18 04:24:34,130] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:24:34,137] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:24:34,137] [INFO] DQC Reference Directory: /var/lib/cwl/stg106890ad-addd-4060-8cc0-3449f22e3492/dqc_reference
[2023-03-18 04:24:35,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:24:35,782] [INFO] Task started: Prodigal
[2023-03-18 04:24:35,782] [INFO] Running command: cat /var/lib/cwl/stge349ebb2-cf85-490a-bfd5-f326980a1126/OceanDNA-a198.fa | prodigal -d OceanDNA-a198/cds.fna -a OceanDNA-a198/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:24:38,529] [INFO] Task succeeded: Prodigal
[2023-03-18 04:24:38,529] [INFO] Task started: HMMsearch
[2023-03-18 04:24:38,529] [INFO] Running command: hmmsearch --tblout OceanDNA-a198/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg106890ad-addd-4060-8cc0-3449f22e3492/dqc_reference/reference_markers.hmm OceanDNA-a198/protein.faa > /dev/null
[2023-03-18 04:24:38,699] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:24:38,699] [WARNING] Found 1/6 markers. [/var/lib/cwl/stge349ebb2-cf85-490a-bfd5-f326980a1126/OceanDNA-a198.fa]
[2023-03-18 04:24:38,713] [INFO] Query marker FASTA was written to OceanDNA-a198/markers.fasta
[2023-03-18 04:24:38,714] [INFO] Task started: Blastn
[2023-03-18 04:24:38,714] [INFO] Running command: blastn -query OceanDNA-a198/markers.fasta -db /var/lib/cwl/stg106890ad-addd-4060-8cc0-3449f22e3492/dqc_reference/reference_markers.fasta -out OceanDNA-a198/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:24:41,794] [INFO] Task succeeded: Blastn
[2023-03-18 04:24:41,797] [INFO] Selected 1 target genomes.
[2023-03-18 04:24:41,797] [INFO] Target genome list was writen to OceanDNA-a198/target_genomes.txt
[2023-03-18 04:24:41,822] [INFO] Task started: fastANI
[2023-03-18 04:24:41,822] [INFO] Running command: fastANI --query /var/lib/cwl/stge349ebb2-cf85-490a-bfd5-f326980a1126/OceanDNA-a198.fa --refList OceanDNA-a198/target_genomes.txt --output OceanDNA-a198/fastani_result.tsv --threads 1
[2023-03-18 04:24:42,071] [INFO] Task succeeded: fastANI
[2023-03-18 04:24:42,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg106890ad-addd-4060-8cc0-3449f22e3492/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:24:42,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg106890ad-addd-4060-8cc0-3449f22e3492/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:24:42,124] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:24:42,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:24:42,124] [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	76.5964	53	149	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:24:42,126] [INFO] DFAST Taxonomy check result was written to OceanDNA-a198/tc_result.tsv
[2023-03-18 04:24:42,129] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:24:42,129] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:24:42,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg106890ad-addd-4060-8cc0-3449f22e3492/dqc_reference/checkm_data
[2023-03-18 04:24:42,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:24:42,140] [INFO] Task started: CheckM
[2023-03-18 04:24:42,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a198/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a198/checkm_input OceanDNA-a198/checkm_result
[2023-03-18 04:24:59,926] [INFO] Task succeeded: CheckM
[2023-03-18 04:24:59,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.70%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 04:24:59,962] [INFO] ===== Completeness check finished =====
[2023-03-18 04:24:59,962] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:24:59,962] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a198/markers.fasta)
[2023-03-18 04:24:59,964] [INFO] Task started: Blastn
[2023-03-18 04:24:59,964] [INFO] Running command: blastn -query OceanDNA-a198/markers.fasta -db /var/lib/cwl/stg106890ad-addd-4060-8cc0-3449f22e3492/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a198/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:25:00,755] [INFO] Task succeeded: Blastn
[2023-03-18 04:25:00,760] [INFO] Selected 5 target genomes.
[2023-03-18 04:25:00,760] [INFO] Target genome list was writen to OceanDNA-a198/target_genomes_gtdb.txt
[2023-03-18 04:25:00,767] [INFO] Task started: fastANI
[2023-03-18 04:25:00,767] [INFO] Running command: fastANI --query /var/lib/cwl/stge349ebb2-cf85-490a-bfd5-f326980a1126/OceanDNA-a198.fa --refList OceanDNA-a198/target_genomes_gtdb.txt --output OceanDNA-a198/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:25:01,659] [INFO] Task succeeded: fastANI
[2023-03-18 04:25:01,664] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:25:01,664] [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_000812185.1	s__Nitrosopelagicus brevis	90.9473	143	149	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.23	96.14	0.93	0.87	7	-
GCA_902511735.1	s__Nitrosopelagicus sp902511735	87.1542	87	149	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647405.1	s__Nitrosopelagicus sp018647405	86.4226	125	149	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	99.40	99.17	0.85	0.83	12	-
GCA_001510295.1	s__Nitrosopelagicus sp001510295	85.9182	96	149	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512865.1	s__Nitrosopelagicus sp902512865	84.5405	64	149	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:25:01,666] [INFO] GTDB search result was written to OceanDNA-a198/result_gtdb.tsv
[2023-03-18 04:25:01,670] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:25:01,674] [INFO] DFAST_QC result json was written to OceanDNA-a198/dqc_result.json
[2023-03-18 04:25:01,674] [INFO] DFAST_QC completed!
[2023-03-18 04:25:01,674] [INFO] Total running time: 0h0m28s