[2023-03-18 09:42:02,233] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:42:02,233] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:42:02,233] [INFO] DQC Reference Directory: /var/lib/cwl/stgf61a6694-f99e-4435-bf3c-db43e151d2d7/dqc_reference
[2023-03-18 09:42:03,327] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:42:03,328] [INFO] Task started: Prodigal
[2023-03-18 09:42:03,328] [INFO] Running command: cat /var/lib/cwl/stg519feb12-5344-4fbe-ae49-15e490b1164e/OceanDNA-b11414.fa | prodigal -d OceanDNA-b11414/cds.fna -a OceanDNA-b11414/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:42:15,498] [INFO] Task succeeded: Prodigal
[2023-03-18 09:42:15,498] [INFO] Task started: HMMsearch
[2023-03-18 09:42:15,498] [INFO] Running command: hmmsearch --tblout OceanDNA-b11414/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf61a6694-f99e-4435-bf3c-db43e151d2d7/dqc_reference/reference_markers.hmm OceanDNA-b11414/protein.faa > /dev/null
[2023-03-18 09:42:15,679] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:42:15,680] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg519feb12-5344-4fbe-ae49-15e490b1164e/OceanDNA-b11414.fa]
[2023-03-18 09:42:15,696] [INFO] Query marker FASTA was written to OceanDNA-b11414/markers.fasta
[2023-03-18 09:42:15,697] [INFO] Task started: Blastn
[2023-03-18 09:42:15,697] [INFO] Running command: blastn -query OceanDNA-b11414/markers.fasta -db /var/lib/cwl/stgf61a6694-f99e-4435-bf3c-db43e151d2d7/dqc_reference/reference_markers.fasta -out OceanDNA-b11414/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:16,225] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:16,226] [INFO] Selected 17 target genomes.
[2023-03-18 09:42:16,226] [INFO] Target genome list was writen to OceanDNA-b11414/target_genomes.txt
[2023-03-18 09:42:16,235] [INFO] Task started: fastANI
[2023-03-18 09:42:16,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg519feb12-5344-4fbe-ae49-15e490b1164e/OceanDNA-b11414.fa --refList OceanDNA-b11414/target_genomes.txt --output OceanDNA-b11414/fastani_result.tsv --threads 1
[2023-03-18 09:42:24,507] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:24,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf61a6694-f99e-4435-bf3c-db43e151d2d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:42:24,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf61a6694-f99e-4435-bf3c-db43e151d2d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:42:24,514] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:42:24,514] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:42:24,515] [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
Winogradskyella aurantiaca	strain=IMCC20180	GCA_003362725.1	2219558	2219558	type	True	88.7643	503	554	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.4261	52	554	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	76.2737	60	554	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.2412	63	554	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.2305	71	554	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.213	56	554	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.1366	59	554	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	76.1292	78	554	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	75.9084	77	554	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	75.7865	69	554	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:42:24,515] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11414/tc_result.tsv
[2023-03-18 09:42:24,515] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:42:24,515] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:42:24,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf61a6694-f99e-4435-bf3c-db43e151d2d7/dqc_reference/checkm_data
[2023-03-18 09:42:24,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:42:24,519] [INFO] Task started: CheckM
[2023-03-18 09:42:24,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11414/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11414/checkm_input OceanDNA-b11414/checkm_result
[2023-03-18 09:42:59,308] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:59,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:59,310] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:59,310] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:59,311] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11414/markers.fasta)
[2023-03-18 09:42:59,311] [INFO] Task started: Blastn
[2023-03-18 09:42:59,311] [INFO] Running command: blastn -query OceanDNA-b11414/markers.fasta -db /var/lib/cwl/stgf61a6694-f99e-4435-bf3c-db43e151d2d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11414/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:59,999] [INFO] Task succeeded: Blastn
[2023-03-18 09:43:00,000] [INFO] Selected 18 target genomes.
[2023-03-18 09:43:00,000] [INFO] Target genome list was writen to OceanDNA-b11414/target_genomes_gtdb.txt
[2023-03-18 09:43:00,039] [INFO] Task started: fastANI
[2023-03-18 09:43:00,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg519feb12-5344-4fbe-ae49-15e490b1164e/OceanDNA-b11414.fa --refList OceanDNA-b11414/target_genomes_gtdb.txt --output OceanDNA-b11414/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:43:09,838] [INFO] Task succeeded: fastANI
[2023-03-18 09:43:09,846] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:43:09,846] [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_003362725.1	s__Winogradskyella aurantiaca	88.7643	503	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709615.1	s__Winogradskyella ouciana	76.2737	60	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	76.159	73	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712105.1	s__Winogradskyella sp003712105	76.139	65	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017581965.1	s__Winogradskyella sp017581965	76.0311	71	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	76.0129	66	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCA_013042245.1	s__Winogradskyella sp013042245	76.0103	52	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	75.9165	56	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099995.1	s__Winogradskyella thalassocola	75.8828	62	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480385.1	s__Winogradskyella sp905480385	75.8556	56	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCA_000171875.1	s__Winogradskyella sp000171875	75.7991	94	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	75.7305	83	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799465.1	s__Psychroserpens sp000799465	75.6204	54	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:43:09,846] [INFO] GTDB search result was written to OceanDNA-b11414/result_gtdb.tsv
[2023-03-18 09:43:09,846] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:43:09,848] [INFO] DFAST_QC result json was written to OceanDNA-b11414/dqc_result.json
[2023-03-18 09:43:09,848] [INFO] DFAST_QC completed!
[2023-03-18 09:43:09,848] [INFO] Total running time: 0h1m8s