[2023-03-15 11:09:10,774] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,774] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg2890ab35-7bd8-473d-a210-f7db781687a4/dqc_reference
[2023-03-15 11:09:12,062] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,062] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,062] [INFO] Running command: cat /var/lib/cwl/stg598cfa47-3f5f-4ab7-b49b-77b03f9b8f1a/OceanDNA-b12282.fa | prodigal -d OceanDNA-b12282/cds.fna -a OceanDNA-b12282/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:24,669] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:24,669] [INFO] Task started: HMMsearch
[2023-03-15 11:09:24,670] [INFO] Running command: hmmsearch --tblout OceanDNA-b12282/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2890ab35-7bd8-473d-a210-f7db781687a4/dqc_reference/reference_markers.hmm OceanDNA-b12282/protein.faa > /dev/null
[2023-03-15 11:09:24,905] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:24,906] [INFO] Found 6/6 markers.
[2023-03-15 11:09:24,920] [INFO] Query marker FASTA was written to OceanDNA-b12282/markers.fasta
[2023-03-15 11:09:24,920] [INFO] Task started: Blastn
[2023-03-15 11:09:24,920] [INFO] Running command: blastn -query OceanDNA-b12282/markers.fasta -db /var/lib/cwl/stg2890ab35-7bd8-473d-a210-f7db781687a4/dqc_reference/reference_markers.fasta -out OceanDNA-b12282/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:25,494] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:25,495] [INFO] Selected 31 target genomes.
[2023-03-15 11:09:25,495] [INFO] Target genome list was writen to OceanDNA-b12282/target_genomes.txt
[2023-03-15 11:09:25,510] [INFO] Task started: fastANI
[2023-03-15 11:09:25,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg598cfa47-3f5f-4ab7-b49b-77b03f9b8f1a/OceanDNA-b12282.fa --refList OceanDNA-b12282/target_genomes.txt --output OceanDNA-b12282/fastani_result.tsv --threads 1
[2023-03-15 11:09:42,391] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:42,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2890ab35-7bd8-473d-a210-f7db781687a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:42,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2890ab35-7bd8-473d-a210-f7db781687a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:42,394] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:42,394] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:42,394] [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
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	75.2596	50	688	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:42,394] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12282/tc_result.tsv
[2023-03-15 11:09:42,395] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:42,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:42,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2890ab35-7bd8-473d-a210-f7db781687a4/dqc_reference/checkm_data
[2023-03-15 11:09:42,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:42,400] [INFO] Task started: CheckM
[2023-03-15 11:09:42,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12282/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12282/checkm_input OceanDNA-b12282/checkm_result
[2023-03-15 11:10:17,475] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:17,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:17,477] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:17,477] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:17,478] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12282/markers.fasta)
[2023-03-15 11:10:17,478] [INFO] Task started: Blastn
[2023-03-15 11:10:17,478] [INFO] Running command: blastn -query OceanDNA-b12282/markers.fasta -db /var/lib/cwl/stg2890ab35-7bd8-473d-a210-f7db781687a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12282/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:18,194] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:18,194] [INFO] Selected 12 target genomes.
[2023-03-15 11:10:18,194] [INFO] Target genome list was writen to OceanDNA-b12282/target_genomes_gtdb.txt
[2023-03-15 11:10:18,203] [INFO] Task started: fastANI
[2023-03-15 11:10:18,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg598cfa47-3f5f-4ab7-b49b-77b03f9b8f1a/OceanDNA-b12282.fa --refList OceanDNA-b12282/target_genomes_gtdb.txt --output OceanDNA-b12282/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:22,643] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:22,649] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:22,650] [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_016780365.1	s__MED-G20 sp016780365	90.2276	511	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_905182745.1	s__MED-G20 sp905182745	89.1848	329	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713405.1	s__MED-G20 sp002713405	87.7637	502	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181675.1	s__MED-G20 sp905181675	82.6373	420	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686655.1	s__MED-G20 sp002686655	78.9413	287	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_905182525.1	s__MED-G20 sp905182525	78.6816	320	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
GCA_002457645.1	s__MED-G20 sp002457645	78.4027	158	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721285.1	s__SP287 sp002721285	77.4123	79	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__SP287	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723085.1	s__GCA-2723085 sp002723085	76.4965	126	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2723085	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:22,650] [INFO] GTDB search result was written to OceanDNA-b12282/result_gtdb.tsv
[2023-03-15 11:10:22,650] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:22,651] [INFO] DFAST_QC result json was written to OceanDNA-b12282/dqc_result.json
[2023-03-15 11:10:22,651] [INFO] DFAST_QC completed!
[2023-03-15 11:10:22,651] [INFO] Total running time: 0h1m12s