[2023-03-17 04:15:14,766] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgff085693-8a7a-4b65-a6fb-4e102cb93867/dqc_reference
[2023-03-17 04:15:16,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,097] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,097] [INFO] Running command: cat /var/lib/cwl/stg33203e1b-7933-43e7-8910-b8f6309d9b24/OceanDNA-b4147.fa | prodigal -d OceanDNA-b4147/cds.fna -a OceanDNA-b4147/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:16:04,134] [INFO] Task succeeded: Prodigal
[2023-03-17 04:16:04,134] [INFO] Task started: HMMsearch
[2023-03-17 04:16:04,134] [INFO] Running command: hmmsearch --tblout OceanDNA-b4147/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff085693-8a7a-4b65-a6fb-4e102cb93867/dqc_reference/reference_markers.hmm OceanDNA-b4147/protein.faa > /dev/null
[2023-03-17 04:16:04,408] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:16:04,408] [INFO] Found 6/6 markers.
[2023-03-17 04:16:04,447] [INFO] Query marker FASTA was written to OceanDNA-b4147/markers.fasta
[2023-03-17 04:16:04,448] [INFO] Task started: Blastn
[2023-03-17 04:16:04,448] [INFO] Running command: blastn -query OceanDNA-b4147/markers.fasta -db /var/lib/cwl/stgff085693-8a7a-4b65-a6fb-4e102cb93867/dqc_reference/reference_markers.fasta -out OceanDNA-b4147/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:04,996] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:04,997] [INFO] Selected 24 target genomes.
[2023-03-17 04:16:04,997] [INFO] Target genome list was writen to OceanDNA-b4147/target_genomes.txt
[2023-03-17 04:16:05,010] [INFO] Task started: fastANI
[2023-03-17 04:16:05,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg33203e1b-7933-43e7-8910-b8f6309d9b24/OceanDNA-b4147.fa --refList OceanDNA-b4147/target_genomes.txt --output OceanDNA-b4147/fastani_result.tsv --threads 1
[2023-03-17 04:16:21,970] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:21,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff085693-8a7a-4b65-a6fb-4e102cb93867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:16:21,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff085693-8a7a-4b65-a6fb-4e102cb93867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:16:21,976] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:16:21,976] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:16:21,976] [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
Roseivirga thermotolerans	strain=CGMCC 1.15111	GCA_014653175.1	1758176	1758176	type	True	76.0687	112	2043	95	below_threshold
Roseivirga spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	76.0654	82	2043	95	below_threshold
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	75.8033	67	2043	95	below_threshold
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	75.7864	92	2043	95	below_threshold
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	75.7759	91	2043	95	below_threshold
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	75.7383	61	2043	95	below_threshold
Roseivirga misakiensis	strain=SK-8	GCA_001747105.1	1563681	1563681	type	True	75.6472	70	2043	95	below_threshold
Roseivirga seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	75.6371	62	2043	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:16:21,977] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4147/tc_result.tsv
[2023-03-17 04:16:21,977] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:16:21,977] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:16:21,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff085693-8a7a-4b65-a6fb-4e102cb93867/dqc_reference/checkm_data
[2023-03-17 04:16:21,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:16:21,985] [INFO] Task started: CheckM
[2023-03-17 04:16:21,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4147/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4147/checkm_input OceanDNA-b4147/checkm_result
[2023-03-17 04:18:17,051] [INFO] Task succeeded: CheckM
[2023-03-17 04:18:17,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:18:17,055] [INFO] ===== Completeness check finished =====
[2023-03-17 04:18:17,055] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:18:17,056] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4147/markers.fasta)
[2023-03-17 04:18:17,057] [INFO] Task started: Blastn
[2023-03-17 04:18:17,057] [INFO] Running command: blastn -query OceanDNA-b4147/markers.fasta -db /var/lib/cwl/stgff085693-8a7a-4b65-a6fb-4e102cb93867/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4147/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:18:17,797] [INFO] Task succeeded: Blastn
[2023-03-17 04:18:17,797] [INFO] Selected 22 target genomes.
[2023-03-17 04:18:17,797] [INFO] Target genome list was writen to OceanDNA-b4147/target_genomes_gtdb.txt
[2023-03-17 04:18:18,128] [INFO] Task started: fastANI
[2023-03-17 04:18:18,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg33203e1b-7933-43e7-8910-b8f6309d9b24/OceanDNA-b4147.fa --refList OceanDNA-b4147/target_genomes_gtdb.txt --output OceanDNA-b4147/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:18:34,263] [INFO] Task succeeded: fastANI
[2023-03-17 04:18:34,269] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:18:34,269] [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_002427745.1	s__Roseivirga sp002427745	77.3325	386	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592825.1	s__Fabibacter sp017592825	76.1509	82	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653175.1	s__Fabibacter thermotolerans	76.0687	112	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	98.67	98.61	0.92	0.91	4	-
GCF_001592965.1	s__Fabibacter spongicola	76.0654	82	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCA_002427755.1	s__Fabibacter sp002427755	76.052	68	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747095.1	s__Fabibacter sp001747095	76.0001	96	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373005.1	s__Fabibacter sp013373005	75.985	87	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111145.1	s__Fabibacter pacificus	75.7864	92	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002786855.1	s__Roseivirga sp002786855	75.7682	64	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	99.94	99.94	0.97	0.97	2	-
GCF_001592945.1	s__Roseivirga seohaensis	75.6371	62	2043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-17 04:18:34,269] [INFO] GTDB search result was written to OceanDNA-b4147/result_gtdb.tsv
[2023-03-17 04:18:34,270] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:18:34,271] [INFO] DFAST_QC result json was written to OceanDNA-b4147/dqc_result.json
[2023-03-17 04:18:34,271] [INFO] DFAST_QC completed!
[2023-03-17 04:18:34,271] [INFO] Total running time: 0h3m20s