[2023-03-15 08:55:06,627] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,628] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dae70f5-8c14-424d-bcb2-162f329f82b0/dqc_reference
[2023-03-15 08:55:08,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,345] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,345] [INFO] Running command: cat /var/lib/cwl/stgd9e4b253-3f6f-4e11-b4d7-c5841646d221/OceanDNA-b11394.fa | prodigal -d OceanDNA-b11394/cds.fna -a OceanDNA-b11394/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:31,003] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:31,004] [INFO] Task started: HMMsearch
[2023-03-15 08:55:31,004] [INFO] Running command: hmmsearch --tblout OceanDNA-b11394/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dae70f5-8c14-424d-bcb2-162f329f82b0/dqc_reference/reference_markers.hmm OceanDNA-b11394/protein.faa > /dev/null
[2023-03-15 08:55:31,273] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:31,274] [INFO] Found 6/6 markers.
[2023-03-15 08:55:31,296] [INFO] Query marker FASTA was written to OceanDNA-b11394/markers.fasta
[2023-03-15 08:55:31,296] [INFO] Task started: Blastn
[2023-03-15 08:55:31,297] [INFO] Running command: blastn -query OceanDNA-b11394/markers.fasta -db /var/lib/cwl/stg2dae70f5-8c14-424d-bcb2-162f329f82b0/dqc_reference/reference_markers.fasta -out OceanDNA-b11394/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:32,009] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:32,010] [INFO] Selected 18 target genomes.
[2023-03-15 08:55:32,010] [INFO] Target genome list was writen to OceanDNA-b11394/target_genomes.txt
[2023-03-15 08:55:32,015] [INFO] Task started: fastANI
[2023-03-15 08:55:32,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9e4b253-3f6f-4e11-b4d7-c5841646d221/OceanDNA-b11394.fa --refList OceanDNA-b11394/target_genomes.txt --output OceanDNA-b11394/fastani_result.tsv --threads 1
[2023-03-15 08:55:48,522] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:48,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dae70f5-8c14-424d-bcb2-162f329f82b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:48,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dae70f5-8c14-424d-bcb2-162f329f82b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:48,533] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:48,533] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:48,533] [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 litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	85.2751	915	1243	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	83.0357	858	1243	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	81.6276	793	1243	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	81.5492	795	1243	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	81.523	770	1243	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	81.19	720	1243	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	81.1774	759	1243	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	80.6108	701	1243	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	80.2459	628	1243	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	80.1646	686	1243	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	79.9052	692	1243	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.8151	671	1243	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.8146	671	1243	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4937	228	1243	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.4289	301	1243	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.1553	199	1243	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0496	218	1243	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.906	179	1243	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:48,533] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11394/tc_result.tsv
[2023-03-15 08:55:48,533] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:48,533] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:48,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dae70f5-8c14-424d-bcb2-162f329f82b0/dqc_reference/checkm_data
[2023-03-15 08:55:48,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:48,573] [INFO] Task started: CheckM
[2023-03-15 08:55:48,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11394/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11394/checkm_input OceanDNA-b11394/checkm_result
[2023-03-15 08:56:45,064] [INFO] Task succeeded: CheckM
[2023-03-15 08:56:45,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:56:45,067] [INFO] ===== Completeness check finished =====
[2023-03-15 08:56:45,068] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:56:45,068] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11394/markers.fasta)
[2023-03-15 08:56:45,069] [INFO] Task started: Blastn
[2023-03-15 08:56:45,069] [INFO] Running command: blastn -query OceanDNA-b11394/markers.fasta -db /var/lib/cwl/stg2dae70f5-8c14-424d-bcb2-162f329f82b0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11394/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:56:46,001] [INFO] Task succeeded: Blastn
[2023-03-15 08:56:46,001] [INFO] Selected 12 target genomes.
[2023-03-15 08:56:46,001] [INFO] Target genome list was writen to OceanDNA-b11394/target_genomes_gtdb.txt
[2023-03-15 08:56:46,013] [INFO] Task started: fastANI
[2023-03-15 08:56:46,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9e4b253-3f6f-4e11-b4d7-c5841646d221/OceanDNA-b11394.fa --refList OceanDNA-b11394/target_genomes_gtdb.txt --output OceanDNA-b11394/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:56,196] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:56,204] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:56:56,204] [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_013249065.1	s__Winogradskyella litoriviva	85.2682	916	1243	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	84.375	868	1243	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	83.0357	858	1243	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	81.6307	793	1243	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	81.5846	791	1243	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	81.5208	771	1243	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	81.4207	730	1243	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	81.1686	760	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_013403915.1	s__Winogradskyella pacifica	81.134	721	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_003387355.1	s__Winogradskyella sediminis	80.2457	628	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCA_016744625.1	s__Winogradskyella sp016744625	80.1163	595	1243	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	79.8112	670	1243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:56,204] [INFO] GTDB search result was written to OceanDNA-b11394/result_gtdb.tsv
[2023-03-15 08:56:56,204] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:56,206] [INFO] DFAST_QC result json was written to OceanDNA-b11394/dqc_result.json
[2023-03-15 08:56:56,206] [INFO] DFAST_QC completed!
[2023-03-15 08:56:56,206] [INFO] Total running time: 0h1m50s