[2023-03-18 21:08:05,357] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:08:05,358] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:08:05,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg143e5361-6a8a-41c5-8366-d5e92a5385e1/dqc_reference
[2023-03-18 21:08:06,462] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:08:06,463] [INFO] Task started: Prodigal
[2023-03-18 21:08:06,463] [INFO] Running command: cat /var/lib/cwl/stgc0504e6a-d799-47a0-9662-daa576e285e6/OceanDNA-b35969.fa | prodigal -d OceanDNA-b35969/cds.fna -a OceanDNA-b35969/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:08:20,247] [INFO] Task succeeded: Prodigal
[2023-03-18 21:08:20,247] [INFO] Task started: HMMsearch
[2023-03-18 21:08:20,247] [INFO] Running command: hmmsearch --tblout OceanDNA-b35969/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg143e5361-6a8a-41c5-8366-d5e92a5385e1/dqc_reference/reference_markers.hmm OceanDNA-b35969/protein.faa > /dev/null
[2023-03-18 21:08:20,424] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:08:20,424] [INFO] Found 6/6 markers.
[2023-03-18 21:08:20,440] [INFO] Query marker FASTA was written to OceanDNA-b35969/markers.fasta
[2023-03-18 21:08:20,440] [INFO] Task started: Blastn
[2023-03-18 21:08:20,440] [INFO] Running command: blastn -query OceanDNA-b35969/markers.fasta -db /var/lib/cwl/stg143e5361-6a8a-41c5-8366-d5e92a5385e1/dqc_reference/reference_markers.fasta -out OceanDNA-b35969/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:08:21,020] [INFO] Task succeeded: Blastn
[2023-03-18 21:08:21,021] [INFO] Selected 30 target genomes.
[2023-03-18 21:08:21,021] [INFO] Target genome list was writen to OceanDNA-b35969/target_genomes.txt
[2023-03-18 21:08:21,030] [INFO] Task started: fastANI
[2023-03-18 21:08:21,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0504e6a-d799-47a0-9662-daa576e285e6/OceanDNA-b35969.fa --refList OceanDNA-b35969/target_genomes.txt --output OceanDNA-b35969/fastani_result.tsv --threads 1
[2023-03-18 21:08:39,027] [INFO] Task succeeded: fastANI
[2023-03-18 21:08:39,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg143e5361-6a8a-41c5-8366-d5e92a5385e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:08:39,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg143e5361-6a8a-41c5-8366-d5e92a5385e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:08:39,031] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:08:39,031] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:08:39,031] [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	77.1944	142	828	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:08:39,031] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35969/tc_result.tsv
[2023-03-18 21:08:39,031] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:08:39,031] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:08:39,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg143e5361-6a8a-41c5-8366-d5e92a5385e1/dqc_reference/checkm_data
[2023-03-18 21:08:39,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:08:39,214] [INFO] Task started: CheckM
[2023-03-18 21:08:39,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35969/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35969/checkm_input OceanDNA-b35969/checkm_result
[2023-03-18 21:09:16,403] [INFO] Task succeeded: CheckM
[2023-03-18 21:09:16,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:09:16,407] [INFO] ===== Completeness check finished =====
[2023-03-18 21:09:16,407] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:09:16,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35969/markers.fasta)
[2023-03-18 21:09:16,408] [INFO] Task started: Blastn
[2023-03-18 21:09:16,408] [INFO] Running command: blastn -query OceanDNA-b35969/markers.fasta -db /var/lib/cwl/stg143e5361-6a8a-41c5-8366-d5e92a5385e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35969/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:09:17,358] [INFO] Task succeeded: Blastn
[2023-03-18 21:09:17,359] [INFO] Selected 17 target genomes.
[2023-03-18 21:09:17,359] [INFO] Target genome list was writen to OceanDNA-b35969/target_genomes_gtdb.txt
[2023-03-18 21:09:17,379] [INFO] Task started: fastANI
[2023-03-18 21:09:17,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0504e6a-d799-47a0-9662-daa576e285e6/OceanDNA-b35969.fa --refList OceanDNA-b35969/target_genomes_gtdb.txt --output OceanDNA-b35969/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:09:24,873] [INFO] Task succeeded: fastANI
[2023-03-18 21:09:24,881] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:09:24,881] [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_002292375.1	s__Cycloclasticus sp002292375	80.9826	279	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066825.1	s__Cycloclasticus sp018066825	78.0272	206	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.96	99.96	0.89	0.89	2	-
GCA_002401365.1	s__Cycloclasticus sp002401365	77.7353	72	828	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	77.4115	120	828	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	77.3531	117	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002101225.1	s__Cycloclasticus sp002101225	77.343	79	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162695.1	s__Cycloclasticus sp002162695	77.2526	135	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	97.08	97.08	0.97	0.97	2	-
GCF_000384415.1	s__Cycloclasticus pugetii	77.2139	141	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	98.68	98.33	0.92	0.87	8	-
GCA_016764415.1	s__Cycloclasticus sp016764415	77.0698	81	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162705.1	s__Cycloclasticus sp002162705	77.068	123	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700385.1	s__Cycloclasticus sp002700385	76.9622	116	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.97	99.95	0.99	0.97	4	-
GCA_001566825.1	s__Cycloclasticus sp001566825	76.849	79	828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	98.53	98.53	0.59	0.59	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:09:24,882] [INFO] GTDB search result was written to OceanDNA-b35969/result_gtdb.tsv
[2023-03-18 21:09:24,882] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:09:24,883] [INFO] DFAST_QC result json was written to OceanDNA-b35969/dqc_result.json
[2023-03-18 21:09:24,884] [INFO] DFAST_QC completed!
[2023-03-18 21:09:24,884] [INFO] Total running time: 0h1m20s