[2023-03-16 17:42:07,080] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:42:07,081] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:42:07,081] [INFO] DQC Reference Directory: /var/lib/cwl/stgb651b6d5-6965-41a8-98da-8b4c80519db1/dqc_reference
[2023-03-16 17:42:08,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:42:08,581] [INFO] Task started: Prodigal
[2023-03-16 17:42:08,581] [INFO] Running command: cat /var/lib/cwl/stg3a774430-ba30-40fd-9d1c-76c9e3046cc9/OceanDNA-a494.fa | prodigal -d OceanDNA-a494/cds.fna -a OceanDNA-a494/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:42:19,272] [INFO] Task succeeded: Prodigal
[2023-03-16 17:42:19,272] [INFO] Task started: HMMsearch
[2023-03-16 17:42:19,272] [INFO] Running command: hmmsearch --tblout OceanDNA-a494/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb651b6d5-6965-41a8-98da-8b4c80519db1/dqc_reference/reference_markers.hmm OceanDNA-a494/protein.faa > /dev/null
[2023-03-16 17:42:19,384] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:42:19,385] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3a774430-ba30-40fd-9d1c-76c9e3046cc9/OceanDNA-a494.fa]
[2023-03-16 17:42:19,396] [INFO] Query marker FASTA was written to OceanDNA-a494/markers.fasta
[2023-03-16 17:42:19,397] [INFO] Task started: Blastn
[2023-03-16 17:42:19,397] [INFO] Running command: blastn -query OceanDNA-a494/markers.fasta -db /var/lib/cwl/stgb651b6d5-6965-41a8-98da-8b4c80519db1/dqc_reference/reference_markers.fasta -out OceanDNA-a494/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:42:19,991] [INFO] Task succeeded: Blastn
[2023-03-16 17:42:19,992] [INFO] Selected 4 target genomes.
[2023-03-16 17:42:19,992] [INFO] Target genome list was writen to OceanDNA-a494/target_genomes.txt
[2023-03-16 17:42:19,994] [INFO] Task started: fastANI
[2023-03-16 17:42:19,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a774430-ba30-40fd-9d1c-76c9e3046cc9/OceanDNA-a494.fa --refList OceanDNA-a494/target_genomes.txt --output OceanDNA-a494/fastani_result.tsv --threads 1
[2023-03-16 17:42:21,635] [INFO] Task succeeded: fastANI
[2023-03-16 17:42:21,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb651b6d5-6965-41a8-98da-8b4c80519db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:42:21,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb651b6d5-6965-41a8-98da-8b4c80519db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:42:21,642] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:42:21,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:42:21,642] [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	86.7623	284	309	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.8567	260	309	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	81.5781	254	309	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	80.7777	232	309	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:42:21,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-a494/tc_result.tsv
[2023-03-16 17:42:21,643] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:42:21,643] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:42:21,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb651b6d5-6965-41a8-98da-8b4c80519db1/dqc_reference/checkm_data
[2023-03-16 17:42:21,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:42:21,647] [INFO] Task started: CheckM
[2023-03-16 17:42:21,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a494/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a494/checkm_input OceanDNA-a494/checkm_result
[2023-03-16 17:42:51,450] [INFO] Task succeeded: CheckM
[2023-03-16 17:42:51,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:42:51,453] [INFO] ===== Completeness check finished =====
[2023-03-16 17:42:51,453] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:42:51,453] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a494/markers.fasta)
[2023-03-16 17:42:51,454] [INFO] Task started: Blastn
[2023-03-16 17:42:51,455] [INFO] Running command: blastn -query OceanDNA-a494/markers.fasta -db /var/lib/cwl/stgb651b6d5-6965-41a8-98da-8b4c80519db1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a494/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:42:52,723] [INFO] Task succeeded: Blastn
[2023-03-16 17:42:52,724] [INFO] Selected 5 target genomes.
[2023-03-16 17:42:52,724] [INFO] Target genome list was writen to OceanDNA-a494/target_genomes_gtdb.txt
[2023-03-16 17:42:52,748] [INFO] Task started: fastANI
[2023-03-16 17:42:52,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a774430-ba30-40fd-9d1c-76c9e3046cc9/OceanDNA-a494.fa --refList OceanDNA-a494/target_genomes_gtdb.txt --output OceanDNA-a494/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:42:55,857] [INFO] Task succeeded: fastANI
[2023-03-16 17:42:55,861] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:42:55,862] [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	91.872	243	309	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	85.3764	251	309	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	84.7075	277	309	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	81.5781	254	309	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	81.4956	260	309	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:42:55,862] [INFO] GTDB search result was written to OceanDNA-a494/result_gtdb.tsv
[2023-03-16 17:42:55,862] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:42:55,863] [INFO] DFAST_QC result json was written to OceanDNA-a494/dqc_result.json
[2023-03-16 17:42:55,864] [INFO] DFAST_QC completed!
[2023-03-16 17:42:55,864] [INFO] Total running time: 0h0m49s