[2023-03-16 07:28:30,043] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,043] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c44a8a7-3dad-43c7-abf2-f83b787de26b/dqc_reference
[2023-03-16 07:28:31,223] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,223] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,223] [INFO] Running command: cat /var/lib/cwl/stg33142cfe-cff3-4410-8a68-e655c55e8bc7/OceanDNA-b8779.fa | prodigal -d OceanDNA-b8779/cds.fna -a OceanDNA-b8779/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:34,689] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:34,689] [INFO] Task started: HMMsearch
[2023-03-16 07:28:34,689] [INFO] Running command: hmmsearch --tblout OceanDNA-b8779/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c44a8a7-3dad-43c7-abf2-f83b787de26b/dqc_reference/reference_markers.hmm OceanDNA-b8779/protein.faa > /dev/null
[2023-03-16 07:28:34,832] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:34,833] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg33142cfe-cff3-4410-8a68-e655c55e8bc7/OceanDNA-b8779.fa]
[2023-03-16 07:28:34,842] [INFO] Query marker FASTA was written to OceanDNA-b8779/markers.fasta
[2023-03-16 07:28:34,843] [INFO] Task started: Blastn
[2023-03-16 07:28:34,843] [INFO] Running command: blastn -query OceanDNA-b8779/markers.fasta -db /var/lib/cwl/stg2c44a8a7-3dad-43c7-abf2-f83b787de26b/dqc_reference/reference_markers.fasta -out OceanDNA-b8779/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:35,276] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:35,278] [INFO] Selected 17 target genomes.
[2023-03-16 07:28:35,279] [INFO] Target genome list was writen to OceanDNA-b8779/target_genomes.txt
[2023-03-16 07:28:35,318] [INFO] Task started: fastANI
[2023-03-16 07:28:35,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg33142cfe-cff3-4410-8a68-e655c55e8bc7/OceanDNA-b8779.fa --refList OceanDNA-b8779/target_genomes.txt --output OceanDNA-b8779/fastani_result.tsv --threads 1
[2023-03-16 07:28:43,623] [INFO] Task succeeded: fastANI
[2023-03-16 07:28:43,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c44a8a7-3dad-43c7-abf2-f83b787de26b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:28:43,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c44a8a7-3dad-43c7-abf2-f83b787de26b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:28:43,624] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:28:43,624] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:28:43,624] [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 07:28:43,625] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8779/tc_result.tsv
[2023-03-16 07:28:43,625] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:28:43,626] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:28:43,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c44a8a7-3dad-43c7-abf2-f83b787de26b/dqc_reference/checkm_data
[2023-03-16 07:28:43,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:28:43,642] [INFO] Task started: CheckM
[2023-03-16 07:28:43,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8779/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8779/checkm_input OceanDNA-b8779/checkm_result
[2023-03-16 07:28:59,279] [INFO] Task succeeded: CheckM
[2023-03-16 07:28:59,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:28:59,282] [INFO] ===== Completeness check finished =====
[2023-03-16 07:28:59,282] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:28:59,283] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8779/markers.fasta)
[2023-03-16 07:28:59,284] [INFO] Task started: Blastn
[2023-03-16 07:28:59,284] [INFO] Running command: blastn -query OceanDNA-b8779/markers.fasta -db /var/lib/cwl/stg2c44a8a7-3dad-43c7-abf2-f83b787de26b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8779/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:59,720] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:59,722] [INFO] Selected 7 target genomes.
[2023-03-16 07:28:59,722] [INFO] Target genome list was writen to OceanDNA-b8779/target_genomes_gtdb.txt
[2023-03-16 07:28:59,829] [INFO] Task started: fastANI
[2023-03-16 07:28:59,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg33142cfe-cff3-4410-8a68-e655c55e8bc7/OceanDNA-b8779.fa --refList OceanDNA-b8779/target_genomes_gtdb.txt --output OceanDNA-b8779/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:01,046] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:01,050] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:29:01,051] [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_902614065.1	s__MED-G14 sp002697465	93.0223	65	78	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.49	95.51	0.88	0.84	14	-
GCA_902586095.1	s__MED-G14 sp902586095	89.4493	50	78	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902544085.1	s__MED-G14 sp902544085	89.404	62	78	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.92	99.92	0.94	0.94	2	-
GCA_902598295.1	s__MED-G14 sp902598295	87.3808	62	78	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526165.1	s__MED-G14 sp902526165	82.5026	51	78	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	95.12	95.12	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:01,052] [INFO] GTDB search result was written to OceanDNA-b8779/result_gtdb.tsv
[2023-03-16 07:29:01,052] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:01,053] [INFO] DFAST_QC result json was written to OceanDNA-b8779/dqc_result.json
[2023-03-16 07:29:01,054] [INFO] DFAST_QC completed!
[2023-03-16 07:29:01,054] [INFO] Total running time: 0h0m31s