[2023-03-17 06:30:49,118] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,118] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d8f2bab-c44c-44c0-b942-7f1b235a26e2/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,292] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stg57462269-8cbe-45e8-b482-9078ebd4dfb6/OceanDNA-a633.fa | prodigal -d OceanDNA-a633/cds.fna -a OceanDNA-a633/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:53,878] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:53,878] [INFO] Task started: HMMsearch
[2023-03-17 06:30:53,878] [INFO] Running command: hmmsearch --tblout OceanDNA-a633/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d8f2bab-c44c-44c0-b942-7f1b235a26e2/dqc_reference/reference_markers.hmm OceanDNA-a633/protein.faa > /dev/null
[2023-03-17 06:30:53,990] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:53,991] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg57462269-8cbe-45e8-b482-9078ebd4dfb6/OceanDNA-a633.fa]
[2023-03-17 06:30:53,998] [INFO] Query marker FASTA was written to OceanDNA-a633/markers.fasta
[2023-03-17 06:30:53,999] [INFO] Task started: Blastn
[2023-03-17 06:30:53,999] [INFO] Running command: blastn -query OceanDNA-a633/markers.fasta -db /var/lib/cwl/stg0d8f2bab-c44c-44c0-b942-7f1b235a26e2/dqc_reference/reference_markers.fasta -out OceanDNA-a633/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:54,433] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:54,433] [INFO] Selected 4 target genomes.
[2023-03-17 06:30:54,433] [INFO] Target genome list was writen to OceanDNA-a633/target_genomes.txt
[2023-03-17 06:30:54,436] [INFO] Task started: fastANI
[2023-03-17 06:30:54,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg57462269-8cbe-45e8-b482-9078ebd4dfb6/OceanDNA-a633.fa --refList OceanDNA-a633/target_genomes.txt --output OceanDNA-a633/fastani_result.tsv --threads 1
[2023-03-17 06:30:55,511] [INFO] Task succeeded: fastANI
[2023-03-17 06:30:55,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d8f2bab-c44c-44c0-b942-7f1b235a26e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:30:55,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d8f2bab-c44c-44c0-b942-7f1b235a26e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:30:55,565] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:30:55,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:30:55,565] [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	81.4237	96	110	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.4215	100	110	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	80.3497	86	110	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	80.1707	95	110	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:30:55,565] [INFO] DFAST Taxonomy check result was written to OceanDNA-a633/tc_result.tsv
[2023-03-17 06:30:55,565] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:30:55,566] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:30:55,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d8f2bab-c44c-44c0-b942-7f1b235a26e2/dqc_reference/checkm_data
[2023-03-17 06:30:55,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:30:55,568] [INFO] Task started: CheckM
[2023-03-17 06:30:55,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a633/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a633/checkm_input OceanDNA-a633/checkm_result
[2023-03-17 06:31:13,325] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:13,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.34%
Contamintation: 2.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:13,326] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:13,326] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:13,327] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a633/markers.fasta)
[2023-03-17 06:31:13,327] [INFO] Task started: Blastn
[2023-03-17 06:31:13,327] [INFO] Running command: blastn -query OceanDNA-a633/markers.fasta -db /var/lib/cwl/stg0d8f2bab-c44c-44c0-b942-7f1b235a26e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a633/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:13,723] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:13,723] [INFO] Selected 5 target genomes.
[2023-03-17 06:31:13,723] [INFO] Target genome list was writen to OceanDNA-a633/target_genomes_gtdb.txt
[2023-03-17 06:31:13,934] [INFO] Task started: fastANI
[2023-03-17 06:31:13,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg57462269-8cbe-45e8-b482-9078ebd4dfb6/OceanDNA-a633.fa --refList OceanDNA-a633/target_genomes_gtdb.txt --output OceanDNA-a633/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:14,823] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:14,827] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:31:14,828] [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_905612295.1	s__Nitrosopumilus sp905612295	98.2107	83	110	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_014384445.1	s__Nitrosopumilus sp014384445	93.529	85	110	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	93.4123	95	110	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.62	95.42	0.85	0.75	5	-
GCA_018657375.1	s__Nitrosopumilus sp018657375	91.7333	81	110	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.79	98.40	0.79	0.75	5	-
GCA_018674605.1	s__Nitrosopumilus sp018674605	86.5721	59	110	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.83	98.50	0.79	0.69	12	-
--------------------------------------------------------------------------------
[2023-03-17 06:31:14,828] [INFO] GTDB search result was written to OceanDNA-a633/result_gtdb.tsv
[2023-03-17 06:31:14,828] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:14,829] [INFO] DFAST_QC result json was written to OceanDNA-a633/dqc_result.json
[2023-03-17 06:31:14,829] [INFO] DFAST_QC completed!
[2023-03-17 06:31:14,829] [INFO] Total running time: 0h0m26s