[2023-03-17 10:48:45,664] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,664] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg14b40244-13af-4dca-8e24-8b9f01eab369/dqc_reference
[2023-03-17 10:48:46,848] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,848] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,848] [INFO] Running command: cat /var/lib/cwl/stg4beff7d3-90cb-4287-bbed-be9eaf3df18c/OceanDNA-b11397.fa | prodigal -d OceanDNA-b11397/cds.fna -a OceanDNA-b11397/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:49:08,712] [INFO] Task succeeded: Prodigal
[2023-03-17 10:49:08,713] [INFO] Task started: HMMsearch
[2023-03-17 10:49:08,713] [INFO] Running command: hmmsearch --tblout OceanDNA-b11397/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14b40244-13af-4dca-8e24-8b9f01eab369/dqc_reference/reference_markers.hmm OceanDNA-b11397/protein.faa > /dev/null
[2023-03-17 10:49:08,949] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:49:08,949] [INFO] Found 6/6 markers.
[2023-03-17 10:49:08,977] [INFO] Query marker FASTA was written to OceanDNA-b11397/markers.fasta
[2023-03-17 10:49:08,978] [INFO] Task started: Blastn
[2023-03-17 10:49:08,978] [INFO] Running command: blastn -query OceanDNA-b11397/markers.fasta -db /var/lib/cwl/stg14b40244-13af-4dca-8e24-8b9f01eab369/dqc_reference/reference_markers.fasta -out OceanDNA-b11397/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:09,610] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:09,611] [INFO] Selected 19 target genomes.
[2023-03-17 10:49:09,612] [INFO] Target genome list was writen to OceanDNA-b11397/target_genomes.txt
[2023-03-17 10:49:09,624] [INFO] Task started: fastANI
[2023-03-17 10:49:09,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg4beff7d3-90cb-4287-bbed-be9eaf3df18c/OceanDNA-b11397.fa --refList OceanDNA-b11397/target_genomes.txt --output OceanDNA-b11397/fastani_result.tsv --threads 1
[2023-03-17 10:49:24,718] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:24,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14b40244-13af-4dca-8e24-8b9f01eab369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:24,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14b40244-13af-4dca-8e24-8b9f01eab369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:24,729] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:24,729] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:49:24,730] [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 thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	83.2824	815	1196	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	82.4812	757	1196	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	82.1151	747	1196	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	82.0514	798	1196	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	82.0087	804	1196	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	81.5179	735	1196	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	80.8484	655	1196	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	80.8451	676	1196	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	80.7773	662	1196	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	80.6696	639	1196	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	80.3858	640	1196	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	80.2308	690	1196	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	80.0384	634	1196	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	80.0333	635	1196	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.0751	221	1196	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8462	210	1196	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.7628	211	1196	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5011	203	1196	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.4507	163	1196	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:49:24,736] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11397/tc_result.tsv
[2023-03-17 10:49:24,736] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:24,736] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:24,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14b40244-13af-4dca-8e24-8b9f01eab369/dqc_reference/checkm_data
[2023-03-17 10:49:24,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:24,744] [INFO] Task started: CheckM
[2023-03-17 10:49:24,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11397/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11397/checkm_input OceanDNA-b11397/checkm_result
[2023-03-17 10:50:19,322] [INFO] Task succeeded: CheckM
[2023-03-17 10:50:19,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:50:19,326] [INFO] ===== Completeness check finished =====
[2023-03-17 10:50:19,326] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:50:19,326] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11397/markers.fasta)
[2023-03-17 10:50:19,327] [INFO] Task started: Blastn
[2023-03-17 10:50:19,327] [INFO] Running command: blastn -query OceanDNA-b11397/markers.fasta -db /var/lib/cwl/stg14b40244-13af-4dca-8e24-8b9f01eab369/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11397/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:50:20,179] [INFO] Task succeeded: Blastn
[2023-03-17 10:50:20,181] [INFO] Selected 16 target genomes.
[2023-03-17 10:50:20,181] [INFO] Target genome list was writen to OceanDNA-b11397/target_genomes_gtdb.txt
[2023-03-17 10:50:20,381] [INFO] Task started: fastANI
[2023-03-17 10:50:20,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg4beff7d3-90cb-4287-bbed-be9eaf3df18c/OceanDNA-b11397.fa --refList OceanDNA-b11397/target_genomes_gtdb.txt --output OceanDNA-b11397/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:50:33,714] [INFO] Task succeeded: fastANI
[2023-03-17 10:50:33,724] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:50:33,724] [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_003386165.1	s__Winogradskyella eximia	97.8528	1116	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	83.6348	798	1196	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	83.2662	817	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	82.4795	737	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_000427335.1	s__Winogradskyella psychrotolerans	82.4684	759	1196	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	82.0952	750	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	82.0687	797	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	82.0276	802	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_013403865.1	s__Winogradskyella costae	81.5274	735	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	81.3303	746	1196	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	80.8484	655	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	80.7689	664	1196	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	80.3717	642	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	80.2377	690	1196	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	80.0282	636	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002364335.1	s__Winogradskyella sp002364335	79.2432	471	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:50:33,725] [INFO] GTDB search result was written to OceanDNA-b11397/result_gtdb.tsv
[2023-03-17 10:50:33,725] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:50:33,728] [INFO] DFAST_QC result json was written to OceanDNA-b11397/dqc_result.json
[2023-03-17 10:50:33,728] [INFO] DFAST_QC completed!
[2023-03-17 10:50:33,728] [INFO] Total running time: 0h1m48s