[2023-03-18 23:44:06,339] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,339] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg29a1e9fb-f190-4851-ba21-60d4b2a6b572/dqc_reference
[2023-03-18 23:44:07,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,447] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,448] [INFO] Running command: cat /var/lib/cwl/stg449e082f-01d6-4148-bc5a-9e305a861e79/OceanDNA-b35974.fa | prodigal -d OceanDNA-b35974/cds.fna -a OceanDNA-b35974/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:18,760] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:18,760] [INFO] Task started: HMMsearch
[2023-03-18 23:44:18,760] [INFO] Running command: hmmsearch --tblout OceanDNA-b35974/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29a1e9fb-f190-4851-ba21-60d4b2a6b572/dqc_reference/reference_markers.hmm OceanDNA-b35974/protein.faa > /dev/null
[2023-03-18 23:44:18,937] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:18,937] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg449e082f-01d6-4148-bc5a-9e305a861e79/OceanDNA-b35974.fa]
[2023-03-18 23:44:18,954] [INFO] Query marker FASTA was written to OceanDNA-b35974/markers.fasta
[2023-03-18 23:44:18,955] [INFO] Task started: Blastn
[2023-03-18 23:44:18,956] [INFO] Running command: blastn -query OceanDNA-b35974/markers.fasta -db /var/lib/cwl/stg29a1e9fb-f190-4851-ba21-60d4b2a6b572/dqc_reference/reference_markers.fasta -out OceanDNA-b35974/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:19,517] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:19,517] [INFO] Selected 19 target genomes.
[2023-03-18 23:44:19,517] [INFO] Target genome list was writen to OceanDNA-b35974/target_genomes.txt
[2023-03-18 23:44:19,531] [INFO] Task started: fastANI
[2023-03-18 23:44:19,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg449e082f-01d6-4148-bc5a-9e305a861e79/OceanDNA-b35974.fa --refList OceanDNA-b35974/target_genomes.txt --output OceanDNA-b35974/fastani_result.tsv --threads 1
[2023-03-18 23:44:30,419] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:30,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29a1e9fb-f190-4851-ba21-60d4b2a6b572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:30,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29a1e9fb-f190-4851-ba21-60d4b2a6b572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:30,423] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:44:30,423] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:44:30,423] [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
Cycloclasticus pugetii	strain=PS-1	GCA_000384415.1	34068	34068	type	True	98.3374	659	689	95	conclusive
--------------------------------------------------------------------------------
[2023-03-18 23:44:30,423] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35974/tc_result.tsv
[2023-03-18 23:44:30,423] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:30,423] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:30,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29a1e9fb-f190-4851-ba21-60d4b2a6b572/dqc_reference/checkm_data
[2023-03-18 23:44:30,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:30,427] [INFO] Task started: CheckM
[2023-03-18 23:44:30,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35974/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35974/checkm_input OceanDNA-b35974/checkm_result
[2023-03-18 23:45:02,470] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:02,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:02,490] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:02,490] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:02,490] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35974/markers.fasta)
[2023-03-18 23:45:02,491] [INFO] Task started: Blastn
[2023-03-18 23:45:02,492] [INFO] Running command: blastn -query OceanDNA-b35974/markers.fasta -db /var/lib/cwl/stg29a1e9fb-f190-4851-ba21-60d4b2a6b572/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35974/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:03,403] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:03,406] [INFO] Selected 19 target genomes.
[2023-03-18 23:45:03,406] [INFO] Target genome list was writen to OceanDNA-b35974/target_genomes_gtdb.txt
[2023-03-18 23:45:03,423] [INFO] Task started: fastANI
[2023-03-18 23:45:03,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg449e082f-01d6-4148-bc5a-9e305a861e79/OceanDNA-b35974.fa --refList OceanDNA-b35974/target_genomes_gtdb.txt --output OceanDNA-b35974/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:12,576] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:12,582] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:45:12,582] [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
GCF_000384415.1	s__Cycloclasticus pugetii	98.3374	659	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	98.68	98.33	0.92	0.87	8	conclusive
GCA_002700385.1	s__Cycloclasticus sp002700385	79.1725	236	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.97	99.95	0.99	0.97	4	-
GCA_002162705.1	s__Cycloclasticus sp002162705	78.1936	173	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960055.1	s__Cycloclasticus sp012960055	77.6334	108	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002101235.1	s__Cycloclasticus sp002101235	77.5664	167	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733135.1	s__Cycloclasticus sp002733135	77.4421	110	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090295.1	s__Cycloclasticus sp019090295	77.3756	85	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401365.1	s__Cycloclasticus sp002401365	77.3665	68	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959695.1	s__Cycloclasticus sp012959695	77.3233	146	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.70	99.70	0.87	0.87	2	-
GCA_002162695.1	s__Cycloclasticus sp002162695	77.2413	118	689	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	97.08	97.08	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:12,583] [INFO] GTDB search result was written to OceanDNA-b35974/result_gtdb.tsv
[2023-03-18 23:45:12,583] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:12,584] [INFO] DFAST_QC result json was written to OceanDNA-b35974/dqc_result.json
[2023-03-18 23:45:12,584] [INFO] DFAST_QC completed!
[2023-03-18 23:45:12,584] [INFO] Total running time: 0h1m6s