[2023-03-16 03:23:47,657] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:47,657] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:47,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg68ec8886-92c2-4a6b-b42b-121b801ce60d/dqc_reference
[2023-03-16 03:23:49,402] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:49,415] [INFO] Task started: Prodigal
[2023-03-16 03:23:49,415] [INFO] Running command: cat /var/lib/cwl/stg7140ed4a-9bc5-43cd-907c-8030bce7ea5b/OceanDNA-b38062.fa | prodigal -d OceanDNA-b38062/cds.fna -a OceanDNA-b38062/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:03,243] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:03,243] [INFO] Task started: HMMsearch
[2023-03-16 03:24:03,243] [INFO] Running command: hmmsearch --tblout OceanDNA-b38062/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68ec8886-92c2-4a6b-b42b-121b801ce60d/dqc_reference/reference_markers.hmm OceanDNA-b38062/protein.faa > /dev/null
[2023-03-16 03:24:03,419] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:03,420] [INFO] Found 6/6 markers.
[2023-03-16 03:24:03,435] [INFO] Query marker FASTA was written to OceanDNA-b38062/markers.fasta
[2023-03-16 03:24:03,436] [INFO] Task started: Blastn
[2023-03-16 03:24:03,436] [INFO] Running command: blastn -query OceanDNA-b38062/markers.fasta -db /var/lib/cwl/stg68ec8886-92c2-4a6b-b42b-121b801ce60d/dqc_reference/reference_markers.fasta -out OceanDNA-b38062/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:04,035] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:04,036] [INFO] Selected 31 target genomes.
[2023-03-16 03:24:04,036] [INFO] Target genome list was writen to OceanDNA-b38062/target_genomes.txt
[2023-03-16 03:24:04,052] [INFO] Task started: fastANI
[2023-03-16 03:24:04,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg7140ed4a-9bc5-43cd-907c-8030bce7ea5b/OceanDNA-b38062.fa --refList OceanDNA-b38062/target_genomes.txt --output OceanDNA-b38062/fastani_result.tsv --threads 1
[2023-03-16 03:24:24,074] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:24,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68ec8886-92c2-4a6b-b42b-121b801ce60d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:24,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68ec8886-92c2-4a6b-b42b-121b801ce60d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:24,074] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:24,074] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:24,074] [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 03:24:24,075] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38062/tc_result.tsv
[2023-03-16 03:24:24,075] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:24,075] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:24,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68ec8886-92c2-4a6b-b42b-121b801ce60d/dqc_reference/checkm_data
[2023-03-16 03:24:24,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:24,081] [INFO] Task started: CheckM
[2023-03-16 03:24:24,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38062/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38062/checkm_input OceanDNA-b38062/checkm_result
[2023-03-16 03:25:01,866] [INFO] Task succeeded: CheckM
[2023-03-16 03:25:01,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:25:01,869] [INFO] ===== Completeness check finished =====
[2023-03-16 03:25:01,869] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:25:01,869] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38062/markers.fasta)
[2023-03-16 03:25:01,869] [INFO] Task started: Blastn
[2023-03-16 03:25:01,869] [INFO] Running command: blastn -query OceanDNA-b38062/markers.fasta -db /var/lib/cwl/stg68ec8886-92c2-4a6b-b42b-121b801ce60d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38062/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:25:02,866] [INFO] Task succeeded: Blastn
[2023-03-16 03:25:02,867] [INFO] Selected 23 target genomes.
[2023-03-16 03:25:02,867] [INFO] Target genome list was writen to OceanDNA-b38062/target_genomes_gtdb.txt
[2023-03-16 03:25:03,569] [INFO] Task started: fastANI
[2023-03-16 03:25:03,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg7140ed4a-9bc5-43cd-907c-8030bce7ea5b/OceanDNA-b38062.fa --refList OceanDNA-b38062/target_genomes_gtdb.txt --output OceanDNA-b38062/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:16,075] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:16,081] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:25:16,082] [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_002390485.1	s__Luminiphilus sp002390485	99.6042	652	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.01	96.90	0.92	0.88	5	conclusive
GCA_018666295.1	s__Luminiphilus sp018666295	94.3166	527	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.15	99.01	0.84	0.82	4	-
GCA_009937065.1	s__Luminiphilus sp009937065	78.1318	129	752	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	77.6747	130	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613175.1	s__Luminiphilus sp902613175	77.6499	90	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689915.1	s__Luminiphilus sp002689915	77.6397	79	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	-
GCA_902547755.1	s__Luminiphilus sp902547755	77.3795	99	752	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	77.3673	118	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524755.1	s__Luminiphilus sp011524755	77.2726	104	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_002469785.1	s__Luminiphilus sp002469785	76.6228	94	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:16,082] [INFO] GTDB search result was written to OceanDNA-b38062/result_gtdb.tsv
[2023-03-16 03:25:16,082] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:16,083] [INFO] DFAST_QC result json was written to OceanDNA-b38062/dqc_result.json
[2023-03-16 03:25:16,083] [INFO] DFAST_QC completed!
[2023-03-16 03:25:16,083] [INFO] Total running time: 0h1m28s