[2023-03-19 02:05:11,579] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,579] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e978987-deeb-4bc4-9395-9ed954b874f6/dqc_reference
[2023-03-19 02:05:13,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,264] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,264] [INFO] Running command: cat /var/lib/cwl/stg6df0f895-06ee-4882-bf78-62602df11aab/OceanDNA-b37917.fa | prodigal -d OceanDNA-b37917/cds.fna -a OceanDNA-b37917/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:23,605] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:23,605] [INFO] Task started: HMMsearch
[2023-03-19 02:05:23,605] [INFO] Running command: hmmsearch --tblout OceanDNA-b37917/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e978987-deeb-4bc4-9395-9ed954b874f6/dqc_reference/reference_markers.hmm OceanDNA-b37917/protein.faa > /dev/null
[2023-03-19 02:05:23,789] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:23,789] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6df0f895-06ee-4882-bf78-62602df11aab/OceanDNA-b37917.fa]
[2023-03-19 02:05:23,802] [INFO] Query marker FASTA was written to OceanDNA-b37917/markers.fasta
[2023-03-19 02:05:23,803] [INFO] Task started: Blastn
[2023-03-19 02:05:23,803] [INFO] Running command: blastn -query OceanDNA-b37917/markers.fasta -db /var/lib/cwl/stg9e978987-deeb-4bc4-9395-9ed954b874f6/dqc_reference/reference_markers.fasta -out OceanDNA-b37917/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:24,371] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:24,372] [INFO] Selected 31 target genomes.
[2023-03-19 02:05:24,372] [INFO] Target genome list was writen to OceanDNA-b37917/target_genomes.txt
[2023-03-19 02:05:24,392] [INFO] Task started: fastANI
[2023-03-19 02:05:24,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg6df0f895-06ee-4882-bf78-62602df11aab/OceanDNA-b37917.fa --refList OceanDNA-b37917/target_genomes.txt --output OceanDNA-b37917/fastani_result.tsv --threads 1
[2023-03-19 02:05:44,471] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:44,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e978987-deeb-4bc4-9395-9ed954b874f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:44,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e978987-deeb-4bc4-9395-9ed954b874f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:44,471] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:44,471] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:05:44,472] [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
--------------------------------------------------------------------------------
[2023-03-19 02:05:44,472] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37917/tc_result.tsv
[2023-03-19 02:05:44,472] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:44,472] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:44,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e978987-deeb-4bc4-9395-9ed954b874f6/dqc_reference/checkm_data
[2023-03-19 02:05:44,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:44,479] [INFO] Task started: CheckM
[2023-03-19 02:05:44,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37917/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37917/checkm_input OceanDNA-b37917/checkm_result
[2023-03-19 02:06:15,090] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:15,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:15,093] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:15,093] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:15,093] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37917/markers.fasta)
[2023-03-19 02:06:15,094] [INFO] Task started: Blastn
[2023-03-19 02:06:15,095] [INFO] Running command: blastn -query OceanDNA-b37917/markers.fasta -db /var/lib/cwl/stg9e978987-deeb-4bc4-9395-9ed954b874f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37917/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:15,975] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:15,976] [INFO] Selected 9 target genomes.
[2023-03-19 02:06:15,976] [INFO] Target genome list was writen to OceanDNA-b37917/target_genomes_gtdb.txt
[2023-03-19 02:06:16,068] [INFO] Task started: fastANI
[2023-03-19 02:06:16,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg6df0f895-06ee-4882-bf78-62602df11aab/OceanDNA-b37917.fa --refList OceanDNA-b37917/target_genomes_gtdb.txt --output OceanDNA-b37917/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:06:20,153] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:20,159] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:06:20,159] [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_011524755.1	s__Luminiphilus sp011524755	92.8414	372	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_003523185.1	s__Luminiphilus sp003523185	90.4818	484	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547755.1	s__Luminiphilus sp902547755	90.4116	402	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862405.1	s__Luminiphilus sp002862405	90.1058	447	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
GCA_902613175.1	s__Luminiphilus sp902613175	89.9315	339	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469785.1	s__Luminiphilus sp002469785	85.5604	376	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937065.1	s__Luminiphilus sp009937065	81.8741	424	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691565.1	s__Luminiphilus sp002691565	81.8338	292	572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
--------------------------------------------------------------------------------
[2023-03-19 02:06:20,159] [INFO] GTDB search result was written to OceanDNA-b37917/result_gtdb.tsv
[2023-03-19 02:06:20,159] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:06:20,160] [INFO] DFAST_QC result json was written to OceanDNA-b37917/dqc_result.json
[2023-03-19 02:06:20,160] [INFO] DFAST_QC completed!
[2023-03-19 02:06:20,160] [INFO] Total running time: 0h1m9s