[2023-03-16 00:05:33,363] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:05:33,364] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:05:33,364] [INFO] DQC Reference Directory: /var/lib/cwl/stg130b0ed0-ad7e-4dd0-9f14-4460fa24e1fe/dqc_reference
[2023-03-16 00:05:34,482] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:05:34,483] [INFO] Task started: Prodigal
[2023-03-16 00:05:34,483] [INFO] Running command: cat /var/lib/cwl/stg0056b101-d2a1-43d3-9d97-4dede708951f/OceanDNA-b36297.fa | prodigal -d OceanDNA-b36297/cds.fna -a OceanDNA-b36297/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:05:40,821] [INFO] Task succeeded: Prodigal
[2023-03-16 00:05:40,822] [INFO] Task started: HMMsearch
[2023-03-16 00:05:40,822] [INFO] Running command: hmmsearch --tblout OceanDNA-b36297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg130b0ed0-ad7e-4dd0-9f14-4460fa24e1fe/dqc_reference/reference_markers.hmm OceanDNA-b36297/protein.faa > /dev/null
[2023-03-16 00:05:41,003] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:05:41,003] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0056b101-d2a1-43d3-9d97-4dede708951f/OceanDNA-b36297.fa]
[2023-03-16 00:05:41,030] [INFO] Query marker FASTA was written to OceanDNA-b36297/markers.fasta
[2023-03-16 00:05:41,031] [INFO] Task started: Blastn
[2023-03-16 00:05:41,031] [INFO] Running command: blastn -query OceanDNA-b36297/markers.fasta -db /var/lib/cwl/stg130b0ed0-ad7e-4dd0-9f14-4460fa24e1fe/dqc_reference/reference_markers.fasta -out OceanDNA-b36297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:05:41,718] [INFO] Task succeeded: Blastn
[2023-03-16 00:05:41,725] [INFO] Selected 28 target genomes.
[2023-03-16 00:05:41,725] [INFO] Target genome list was writen to OceanDNA-b36297/target_genomes.txt
[2023-03-16 00:05:41,739] [INFO] Task started: fastANI
[2023-03-16 00:05:41,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg0056b101-d2a1-43d3-9d97-4dede708951f/OceanDNA-b36297.fa --refList OceanDNA-b36297/target_genomes.txt --output OceanDNA-b36297/fastani_result.tsv --threads 1
[2023-03-16 00:05:55,376] [INFO] Task succeeded: fastANI
[2023-03-16 00:05:55,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg130b0ed0-ad7e-4dd0-9f14-4460fa24e1fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:05:55,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg130b0ed0-ad7e-4dd0-9f14-4460fa24e1fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:05:55,377] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:05:55,377] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:05:55,377] [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 00:05:55,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36297/tc_result.tsv
[2023-03-16 00:05:55,388] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:05:55,388] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:05:55,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg130b0ed0-ad7e-4dd0-9f14-4460fa24e1fe/dqc_reference/checkm_data
[2023-03-16 00:05:55,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:05:55,621] [INFO] Task started: CheckM
[2023-03-16 00:05:55,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36297/checkm_input OceanDNA-b36297/checkm_result
[2023-03-16 00:06:19,933] [INFO] Task succeeded: CheckM
[2023-03-16 00:06:19,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:06:19,957] [INFO] ===== Completeness check finished =====
[2023-03-16 00:06:19,957] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:06:19,958] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36297/markers.fasta)
[2023-03-16 00:06:19,959] [INFO] Task started: Blastn
[2023-03-16 00:06:19,959] [INFO] Running command: blastn -query OceanDNA-b36297/markers.fasta -db /var/lib/cwl/stg130b0ed0-ad7e-4dd0-9f14-4460fa24e1fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:06:21,004] [INFO] Task succeeded: Blastn
[2023-03-16 00:06:21,023] [INFO] Selected 17 target genomes.
[2023-03-16 00:06:21,023] [INFO] Target genome list was writen to OceanDNA-b36297/target_genomes_gtdb.txt
[2023-03-16 00:06:21,037] [INFO] Task started: fastANI
[2023-03-16 00:06:21,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg0056b101-d2a1-43d3-9d97-4dede708951f/OceanDNA-b36297.fa --refList OceanDNA-b36297/target_genomes_gtdb.txt --output OceanDNA-b36297/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:06:28,039] [INFO] Task succeeded: fastANI
[2023-03-16 00:06:28,046] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:06:28,047] [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_011053005.1	s__GCA-002733105 sp011053005	78.5923	187	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163085.1	s__41-12-T18 sp002163085	76.8879	60	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215775.1	s__GCA-002733105 sp013215775	76.8349	75	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733715.2	s__GCA-002733105 sp002733715	76.7364	56	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139345.1	s__GCA-002733105 sp013139345	76.7325	67	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733335.1	s__GCA-002733105 sp002733335	76.6272	67	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733105.1	s__GCA-002733105 sp002733105	76.483	50	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215825.1	s__GCA-002733105 sp013215825	76.3991	91	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859375.1	s__GCA-002733105 sp014859375	76.3739	58	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	76.3308	60	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733505.1	s__GCA-002733105 sp002733505	76.3209	61	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:06:28,047] [INFO] GTDB search result was written to OceanDNA-b36297/result_gtdb.tsv
[2023-03-16 00:06:28,047] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:06:28,052] [INFO] DFAST_QC result json was written to OceanDNA-b36297/dqc_result.json
[2023-03-16 00:06:28,052] [INFO] DFAST_QC completed!
[2023-03-16 00:06:28,052] [INFO] Total running time: 0h0m55s