[2023-03-15 13:03:53,448] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,448] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,448] [INFO] DQC Reference Directory: /var/lib/cwl/stgf11d5b3b-57aa-4eac-900c-6c51b15bbca4/dqc_reference
[2023-03-15 13:03:54,660] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,660] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,660] [INFO] Running command: cat /var/lib/cwl/stg56c56e41-42e4-4f8a-80db-e6a7cde45da2/OceanDNA-b38152.fa | prodigal -d OceanDNA-b38152/cds.fna -a OceanDNA-b38152/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:04,439] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:04,439] [INFO] Task started: HMMsearch
[2023-03-15 13:04:04,439] [INFO] Running command: hmmsearch --tblout OceanDNA-b38152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf11d5b3b-57aa-4eac-900c-6c51b15bbca4/dqc_reference/reference_markers.hmm OceanDNA-b38152/protein.faa > /dev/null
[2023-03-15 13:04:04,642] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:04,643] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg56c56e41-42e4-4f8a-80db-e6a7cde45da2/OceanDNA-b38152.fa]
[2023-03-15 13:04:04,658] [INFO] Query marker FASTA was written to OceanDNA-b38152/markers.fasta
[2023-03-15 13:04:04,658] [INFO] Task started: Blastn
[2023-03-15 13:04:04,658] [INFO] Running command: blastn -query OceanDNA-b38152/markers.fasta -db /var/lib/cwl/stgf11d5b3b-57aa-4eac-900c-6c51b15bbca4/dqc_reference/reference_markers.fasta -out OceanDNA-b38152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:05,114] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:05,115] [INFO] Selected 23 target genomes.
[2023-03-15 13:04:05,115] [INFO] Target genome list was writen to OceanDNA-b38152/target_genomes.txt
[2023-03-15 13:04:05,131] [INFO] Task started: fastANI
[2023-03-15 13:04:05,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg56c56e41-42e4-4f8a-80db-e6a7cde45da2/OceanDNA-b38152.fa --refList OceanDNA-b38152/target_genomes.txt --output OceanDNA-b38152/fastani_result.tsv --threads 1
[2023-03-15 13:04:20,863] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:20,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf11d5b3b-57aa-4eac-900c-6c51b15bbca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:20,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf11d5b3b-57aa-4eac-900c-6c51b15bbca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:20,863] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:20,864] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:20,864] [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
--------------------------------------------------------------------------------
[2023-03-15 13:04:20,864] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38152/tc_result.tsv
[2023-03-15 13:04:20,864] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:20,864] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:20,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf11d5b3b-57aa-4eac-900c-6c51b15bbca4/dqc_reference/checkm_data
[2023-03-15 13:04:20,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:20,870] [INFO] Task started: CheckM
[2023-03-15 13:04:20,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38152/checkm_input OceanDNA-b38152/checkm_result
[2023-03-15 13:04:50,449] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:50,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:50,452] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:50,452] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:50,452] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38152/markers.fasta)
[2023-03-15 13:04:50,452] [INFO] Task started: Blastn
[2023-03-15 13:04:50,452] [INFO] Running command: blastn -query OceanDNA-b38152/markers.fasta -db /var/lib/cwl/stgf11d5b3b-57aa-4eac-900c-6c51b15bbca4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:50,913] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:50,914] [INFO] Selected 22 target genomes.
[2023-03-15 13:04:50,914] [INFO] Target genome list was writen to OceanDNA-b38152/target_genomes_gtdb.txt
[2023-03-15 13:04:50,992] [INFO] Task started: fastANI
[2023-03-15 13:04:50,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg56c56e41-42e4-4f8a-80db-e6a7cde45da2/OceanDNA-b38152.fa --refList OceanDNA-b38152/target_genomes_gtdb.txt --output OceanDNA-b38152/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:05:02,050] [INFO] Task succeeded: fastANI
[2023-03-15 13:05:02,057] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:05:02,058] [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_002705465.1	s__Luminiphilus sp002705465	99.3776	257	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011523115.1	s__Luminiphilus sp011523115	94.0841	335	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518075.1	s__Luminiphilus sp902518075	79.1649	67	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778085.1	s__Luminiphilus sp016778085	78.701	88	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222695.1	s__Luminiphilus sp018222695	78.0209	96	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331685.1	s__Luminiphilus sp003331685	77.9205	58	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520195.1	s__Luminiphilus sp902520195	77.7257	103	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.03	95.89	0.61	0.58	3	-
GCA_002377985.1	s__Luminiphilus sp002377985	77.5638	76	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623175.1	s__Luminiphilus sp902623175	77.5074	93	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721785.1	s__Luminiphilus sp002721785	77.3333	105	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
GCA_008081075.1	s__Luminiphilus sp008081075	77.1863	52	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683395.1	s__Luminiphilus sp002683395	76.9015	80	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.62	98.62	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:05:02,058] [INFO] GTDB search result was written to OceanDNA-b38152/result_gtdb.tsv
[2023-03-15 13:05:02,058] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:05:02,059] [INFO] DFAST_QC result json was written to OceanDNA-b38152/dqc_result.json
[2023-03-15 13:05:02,059] [INFO] DFAST_QC completed!
[2023-03-15 13:05:02,059] [INFO] Total running time: 0h1m9s