[2023-03-18 00:53:42,426] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,426] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg57e4b1b1-99ce-4cf7-b99e-27bcbe182379/dqc_reference
[2023-03-18 00:53:43,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,584] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,584] [INFO] Running command: cat /var/lib/cwl/stg996a0787-5ccf-4391-be0e-37860b59a209/OceanDNA-b38083.fa | prodigal -d OceanDNA-b38083/cds.fna -a OceanDNA-b38083/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:57,336] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:57,337] [INFO] Task started: HMMsearch
[2023-03-18 00:53:57,337] [INFO] Running command: hmmsearch --tblout OceanDNA-b38083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57e4b1b1-99ce-4cf7-b99e-27bcbe182379/dqc_reference/reference_markers.hmm OceanDNA-b38083/protein.faa > /dev/null
[2023-03-18 00:53:57,519] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:57,519] [INFO] Found 6/6 markers.
[2023-03-18 00:53:57,544] [INFO] Query marker FASTA was written to OceanDNA-b38083/markers.fasta
[2023-03-18 00:53:57,545] [INFO] Task started: Blastn
[2023-03-18 00:53:57,545] [INFO] Running command: blastn -query OceanDNA-b38083/markers.fasta -db /var/lib/cwl/stg57e4b1b1-99ce-4cf7-b99e-27bcbe182379/dqc_reference/reference_markers.fasta -out OceanDNA-b38083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:58,147] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:58,148] [INFO] Selected 27 target genomes.
[2023-03-18 00:53:58,148] [INFO] Target genome list was writen to OceanDNA-b38083/target_genomes.txt
[2023-03-18 00:53:58,164] [INFO] Task started: fastANI
[2023-03-18 00:53:58,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg996a0787-5ccf-4391-be0e-37860b59a209/OceanDNA-b38083.fa --refList OceanDNA-b38083/target_genomes.txt --output OceanDNA-b38083/fastani_result.tsv --threads 1
[2023-03-18 00:54:14,279] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:14,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57e4b1b1-99ce-4cf7-b99e-27bcbe182379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:14,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57e4b1b1-99ce-4cf7-b99e-27bcbe182379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:14,280] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:14,280] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:54:14,280] [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
--------------------------------------------------------------------------------
[2023-03-18 00:54:14,283] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38083/tc_result.tsv
[2023-03-18 00:54:14,287] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:14,287] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:14,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57e4b1b1-99ce-4cf7-b99e-27bcbe182379/dqc_reference/checkm_data
[2023-03-18 00:54:14,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:14,304] [INFO] Task started: CheckM
[2023-03-18 00:54:14,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38083/checkm_input OceanDNA-b38083/checkm_result
[2023-03-18 00:54:52,119] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:52,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:52,150] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:52,150] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:52,150] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38083/markers.fasta)
[2023-03-18 00:54:52,151] [INFO] Task started: Blastn
[2023-03-18 00:54:52,151] [INFO] Running command: blastn -query OceanDNA-b38083/markers.fasta -db /var/lib/cwl/stg57e4b1b1-99ce-4cf7-b99e-27bcbe182379/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:53,213] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:53,214] [INFO] Selected 23 target genomes.
[2023-03-18 00:54:53,214] [INFO] Target genome list was writen to OceanDNA-b38083/target_genomes_gtdb.txt
[2023-03-18 00:54:53,240] [INFO] Task started: fastANI
[2023-03-18 00:54:53,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg996a0787-5ccf-4391-be0e-37860b59a209/OceanDNA-b38083.fa --refList OceanDNA-b38083/target_genomes_gtdb.txt --output OceanDNA-b38083/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:55:04,559] [INFO] Task succeeded: fastANI
[2023-03-18 00:55:04,564] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:55:04,565] [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_002456975.1	s__Luminiphilus sp002456975	99.6264	590	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.72	99.71	0.90	0.87	3	conclusive
GCA_002862405.1	s__Luminiphilus sp002862405	78.8099	65	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
GCA_902547755.1	s__Luminiphilus sp902547755	78.0442	67	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523185.1	s__Luminiphilus sp003523185	77.5403	72	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000227505.4	s__Luminiphilus sp000227505	77.4189	79	771	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	77.0496	52	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
GCA_002689915.1	s__Luminiphilus sp002689915	77.0212	51	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	-
GCA_018666295.1	s__Luminiphilus sp018666295	76.8474	54	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.15	99.01	0.84	0.82	4	-
--------------------------------------------------------------------------------
[2023-03-18 00:55:04,565] [INFO] GTDB search result was written to OceanDNA-b38083/result_gtdb.tsv
[2023-03-18 00:55:04,565] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:55:04,566] [INFO] DFAST_QC result json was written to OceanDNA-b38083/dqc_result.json
[2023-03-18 00:55:04,566] [INFO] DFAST_QC completed!
[2023-03-18 00:55:04,566] [INFO] Total running time: 0h1m22s