[2023-03-16 19:19:41,321] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:19:41,321] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:19:41,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgd52cd440-8227-4143-8e3e-7eff3d52cef9/dqc_reference
[2023-03-16 19:19:42,714] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:19:42,715] [INFO] Task started: Prodigal
[2023-03-16 19:19:42,715] [INFO] Running command: cat /var/lib/cwl/stg8191b695-0bbe-4f03-b165-2b4554afa1c1/OceanDNA-b11419.fa | prodigal -d OceanDNA-b11419/cds.fna -a OceanDNA-b11419/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:20:06,431] [INFO] Task succeeded: Prodigal
[2023-03-16 19:20:06,431] [INFO] Task started: HMMsearch
[2023-03-16 19:20:06,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b11419/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd52cd440-8227-4143-8e3e-7eff3d52cef9/dqc_reference/reference_markers.hmm OceanDNA-b11419/protein.faa > /dev/null
[2023-03-16 19:20:06,606] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:20:06,606] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8191b695-0bbe-4f03-b165-2b4554afa1c1/OceanDNA-b11419.fa]
[2023-03-16 19:20:06,626] [INFO] Query marker FASTA was written to OceanDNA-b11419/markers.fasta
[2023-03-16 19:20:06,628] [INFO] Task started: Blastn
[2023-03-16 19:20:06,628] [INFO] Running command: blastn -query OceanDNA-b11419/markers.fasta -db /var/lib/cwl/stgd52cd440-8227-4143-8e3e-7eff3d52cef9/dqc_reference/reference_markers.fasta -out OceanDNA-b11419/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:20:07,188] [INFO] Task succeeded: Blastn
[2023-03-16 19:20:07,189] [INFO] Selected 16 target genomes.
[2023-03-16 19:20:07,189] [INFO] Target genome list was writen to OceanDNA-b11419/target_genomes.txt
[2023-03-16 19:20:07,202] [INFO] Task started: fastANI
[2023-03-16 19:20:07,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg8191b695-0bbe-4f03-b165-2b4554afa1c1/OceanDNA-b11419.fa --refList OceanDNA-b11419/target_genomes.txt --output OceanDNA-b11419/fastani_result.tsv --threads 1
[2023-03-16 19:20:18,341] [INFO] Task succeeded: fastANI
[2023-03-16 19:20:18,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd52cd440-8227-4143-8e3e-7eff3d52cef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:20:18,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd52cd440-8227-4143-8e3e-7eff3d52cef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:20:18,351] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:20:18,352] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:20:18,352] [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 echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.4378	463	872	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.4326	463	872	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.9799	409	872	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.9454	430	872	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.9419	399	872	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.8412	428	872	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	78.8208	386	872	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.6107	380	872	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.6046	347	872	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.5711	386	872	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	78.1803	350	872	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.2587	211	872	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.6657	157	872	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.5779	147	872	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.5569	121	872	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	75.9491	53	872	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:20:18,353] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11419/tc_result.tsv
[2023-03-16 19:20:18,353] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:20:18,354] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:20:18,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd52cd440-8227-4143-8e3e-7eff3d52cef9/dqc_reference/checkm_data
[2023-03-16 19:20:18,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:20:18,426] [INFO] Task started: CheckM
[2023-03-16 19:20:18,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11419/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11419/checkm_input OceanDNA-b11419/checkm_result
[2023-03-16 19:21:11,373] [INFO] Task succeeded: CheckM
[2023-03-16 19:21:11,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:21:11,379] [INFO] ===== Completeness check finished =====
[2023-03-16 19:21:11,379] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:21:11,379] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11419/markers.fasta)
[2023-03-16 19:21:11,380] [INFO] Task started: Blastn
[2023-03-16 19:21:11,380] [INFO] Running command: blastn -query OceanDNA-b11419/markers.fasta -db /var/lib/cwl/stgd52cd440-8227-4143-8e3e-7eff3d52cef9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11419/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:21:12,142] [INFO] Task succeeded: Blastn
[2023-03-16 19:21:12,144] [INFO] Selected 11 target genomes.
[2023-03-16 19:21:12,145] [INFO] Target genome list was writen to OceanDNA-b11419/target_genomes_gtdb.txt
[2023-03-16 19:21:12,157] [INFO] Task started: fastANI
[2023-03-16 19:21:12,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg8191b695-0bbe-4f03-b165-2b4554afa1c1/OceanDNA-b11419.fa --refList OceanDNA-b11419/target_genomes_gtdb.txt --output OceanDNA-b11419/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:21:20,064] [INFO] Task succeeded: fastANI
[2023-03-16 19:21:20,071] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:21:20,071] [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_002364335.1	s__Winogradskyella sp002364335	99.866	848	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016744625.1	s__Winogradskyella sp016744625	80.08	491	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	79.4271	464	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000171875.1	s__Winogradskyella sp000171875	79.3722	459	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	79.2367	444	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	79.2123	453	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	78.9572	429	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	78.9419	399	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645385.1	s__Winogradskyella sp015645385	78.8322	385	872	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	78.816	429	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	78.6046	347	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:21:20,072] [INFO] GTDB search result was written to OceanDNA-b11419/result_gtdb.tsv
[2023-03-16 19:21:20,073] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:21:20,076] [INFO] DFAST_QC result json was written to OceanDNA-b11419/dqc_result.json
[2023-03-16 19:21:20,076] [INFO] DFAST_QC completed!
[2023-03-16 19:21:20,076] [INFO] Total running time: 0h1m39s