[2023-03-16 01:12:29,294] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,294] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg287d9d4d-e934-4f36-982d-932f4ca4f1c6/dqc_reference
[2023-03-16 01:12:30,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,462] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,462] [INFO] Running command: cat /var/lib/cwl/stgb571f133-395c-49fc-84e0-b322fbbd2dee/OceanDNA-b45782.fa | prodigal -d OceanDNA-b45782/cds.fna -a OceanDNA-b45782/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:54,068] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:54,068] [INFO] Task started: HMMsearch
[2023-03-16 01:12:54,068] [INFO] Running command: hmmsearch --tblout OceanDNA-b45782/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg287d9d4d-e934-4f36-982d-932f4ca4f1c6/dqc_reference/reference_markers.hmm OceanDNA-b45782/protein.faa > /dev/null
[2023-03-16 01:12:54,263] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:54,263] [INFO] Found 6/6 markers.
[2023-03-16 01:12:54,286] [INFO] Query marker FASTA was written to OceanDNA-b45782/markers.fasta
[2023-03-16 01:12:54,288] [INFO] Task started: Blastn
[2023-03-16 01:12:54,288] [INFO] Running command: blastn -query OceanDNA-b45782/markers.fasta -db /var/lib/cwl/stg287d9d4d-e934-4f36-982d-932f4ca4f1c6/dqc_reference/reference_markers.fasta -out OceanDNA-b45782/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:54,859] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:54,872] [INFO] Selected 9 target genomes.
[2023-03-16 01:12:54,872] [INFO] Target genome list was writen to OceanDNA-b45782/target_genomes.txt
[2023-03-16 01:12:54,893] [INFO] Task started: fastANI
[2023-03-16 01:12:54,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgb571f133-395c-49fc-84e0-b322fbbd2dee/OceanDNA-b45782.fa --refList OceanDNA-b45782/target_genomes.txt --output OceanDNA-b45782/fastani_result.tsv --threads 1
[2023-03-16 01:13:00,300] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:00,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg287d9d4d-e934-4f36-982d-932f4ca4f1c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:13:00,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg287d9d4d-e934-4f36-982d-932f4ca4f1c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:13:00,301] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:13:00,301] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:13:00,301] [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
--------------------------------------------------------------------------------
[2023-03-16 01:13:00,304] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45782/tc_result.tsv
[2023-03-16 01:13:00,306] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:13:00,306] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:13:00,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg287d9d4d-e934-4f36-982d-932f4ca4f1c6/dqc_reference/checkm_data
[2023-03-16 01:13:00,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:13:00,313] [INFO] Task started: CheckM
[2023-03-16 01:13:00,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45782/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45782/checkm_input OceanDNA-b45782/checkm_result
[2023-03-16 01:14:01,882] [INFO] Task succeeded: CheckM
[2023-03-16 01:14:01,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.65%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-03-16 01:14:01,886] [INFO] ===== Completeness check finished =====
[2023-03-16 01:14:01,886] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:14:01,887] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45782/markers.fasta)
[2023-03-16 01:14:01,887] [INFO] Task started: Blastn
[2023-03-16 01:14:01,888] [INFO] Running command: blastn -query OceanDNA-b45782/markers.fasta -db /var/lib/cwl/stg287d9d4d-e934-4f36-982d-932f4ca4f1c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45782/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:14:02,866] [INFO] Task succeeded: Blastn
[2023-03-16 01:14:02,867] [INFO] Selected 23 target genomes.
[2023-03-16 01:14:02,868] [INFO] Target genome list was writen to OceanDNA-b45782/target_genomes_gtdb.txt
[2023-03-16 01:14:03,100] [INFO] Task started: fastANI
[2023-03-16 01:14:03,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgb571f133-395c-49fc-84e0-b322fbbd2dee/OceanDNA-b45782.fa --refList OceanDNA-b45782/target_genomes_gtdb.txt --output OceanDNA-b45782/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:14:14,218] [INFO] Task succeeded: fastANI
[2023-03-16 01:14:14,222] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:14:14,223] [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_002692605.1	s__MB11C04 sp002692605	98.3215	652	840	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.46	98.03	0.81	0.78	7	conclusive
GCA_002167605.1	s__MB11C04 sp002167605	80.2243	427	840	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.01	99.01	0.79	0.79	2	-
GCA_002171765.1	s__MB11C04 sp002171765	76.9256	52	840	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.33	98.33	0.72	0.72	2	-
GCA_018645725.1	s__MB11C04 sp018645725	76.5999	86	840	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364975.1	s__MB11C04 sp002364975	76.3975	57	840	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.20	99.18	0.88	0.87	3	-
GCA_002722545.1	s__MB11C04 sp002722545	76.3085	65	840	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:14:14,223] [INFO] GTDB search result was written to OceanDNA-b45782/result_gtdb.tsv
[2023-03-16 01:14:14,223] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:14:14,224] [INFO] DFAST_QC result json was written to OceanDNA-b45782/dqc_result.json
[2023-03-16 01:14:14,224] [INFO] DFAST_QC completed!
[2023-03-16 01:14:14,224] [INFO] Total running time: 0h1m45s