[2023-03-18 03:45:10,275] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,275] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f281394-8262-4798-9c9b-3157d26a69b5/dqc_reference
[2023-03-18 03:45:12,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,144] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,144] [INFO] Running command: cat /var/lib/cwl/stg6058dc89-21ae-45e2-8f99-4b20d465ef3c/OceanDNA-b7352.fa | prodigal -d OceanDNA-b7352/cds.fna -a OceanDNA-b7352/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:24,799] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:24,799] [INFO] Task started: HMMsearch
[2023-03-18 03:45:24,799] [INFO] Running command: hmmsearch --tblout OceanDNA-b7352/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f281394-8262-4798-9c9b-3157d26a69b5/dqc_reference/reference_markers.hmm OceanDNA-b7352/protein.faa > /dev/null
[2023-03-18 03:45:25,016] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:25,017] [INFO] Found 6/6 markers.
[2023-03-18 03:45:25,031] [INFO] Query marker FASTA was written to OceanDNA-b7352/markers.fasta
[2023-03-18 03:45:25,031] [INFO] Task started: Blastn
[2023-03-18 03:45:25,031] [INFO] Running command: blastn -query OceanDNA-b7352/markers.fasta -db /var/lib/cwl/stg8f281394-8262-4798-9c9b-3157d26a69b5/dqc_reference/reference_markers.fasta -out OceanDNA-b7352/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:25,672] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:25,673] [INFO] Selected 29 target genomes.
[2023-03-18 03:45:25,673] [INFO] Target genome list was writen to OceanDNA-b7352/target_genomes.txt
[2023-03-18 03:45:25,688] [INFO] Task started: fastANI
[2023-03-18 03:45:25,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg6058dc89-21ae-45e2-8f99-4b20d465ef3c/OceanDNA-b7352.fa --refList OceanDNA-b7352/target_genomes.txt --output OceanDNA-b7352/fastani_result.tsv --threads 1
[2023-03-18 03:45:42,773] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:42,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f281394-8262-4798-9c9b-3157d26a69b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:42,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f281394-8262-4798-9c9b-3157d26a69b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:42,789] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:42,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:42,790] [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
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	76.8679	56	634	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.7783	82	634	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.773	90	634	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.7721	90	634	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	76.7721	90	634	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.6752	73	634	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	76.4522	79	634	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.4432	94	634	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.3999	99	634	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.3996	102	634	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.3418	89	634	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.3247	90	634	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	76.293	90	634	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.2925	102	634	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	76.2747	90	634	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.2547	104	634	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.2184	106	634	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	76.1733	88	634	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	76.1727	78	634	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.1401	70	634	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.1348	98	634	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.0921	93	634	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.0921	93	634	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.0636	90	634	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	76.0431	75	634	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.0012	100	634	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	75.9087	61	634	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	75.8742	59	634	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	75.8446	55	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:42,790] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7352/tc_result.tsv
[2023-03-18 03:45:42,790] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:42,790] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:42,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f281394-8262-4798-9c9b-3157d26a69b5/dqc_reference/checkm_data
[2023-03-18 03:45:42,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:42,794] [INFO] Task started: CheckM
[2023-03-18 03:45:42,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7352/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7352/checkm_input OceanDNA-b7352/checkm_result
[2023-03-18 03:46:18,205] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:18,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.55%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:18,208] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:18,208] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:18,208] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7352/markers.fasta)
[2023-03-18 03:46:18,209] [INFO] Task started: Blastn
[2023-03-18 03:46:18,209] [INFO] Running command: blastn -query OceanDNA-b7352/markers.fasta -db /var/lib/cwl/stg8f281394-8262-4798-9c9b-3157d26a69b5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7352/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:19,052] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:19,053] [INFO] Selected 10 target genomes.
[2023-03-18 03:46:19,053] [INFO] Target genome list was writen to OceanDNA-b7352/target_genomes_gtdb.txt
[2023-03-18 03:46:19,122] [INFO] Task started: fastANI
[2023-03-18 03:46:19,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg6058dc89-21ae-45e2-8f99-4b20d465ef3c/OceanDNA-b7352.fa --refList OceanDNA-b7352/target_genomes_gtdb.txt --output OceanDNA-b7352/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:23,555] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:23,562] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:46:23,562] [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_018608765.1	s__Hel1-33-131 sp018608765	82.328	432	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	82.1748	487	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	81.5299	347	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	81.1587	395	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	80.9965	363	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	80.5475	385	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	78.7699	233	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	78.5407	259	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCF_014297365.1	s__Winogradskyella echinorum	76.0921	93	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000211855.2	s__Lacinutrix sp000211855	75.9791	96	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:23,562] [INFO] GTDB search result was written to OceanDNA-b7352/result_gtdb.tsv
[2023-03-18 03:46:23,562] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:23,564] [INFO] DFAST_QC result json was written to OceanDNA-b7352/dqc_result.json
[2023-03-18 03:46:23,565] [INFO] DFAST_QC completed!
[2023-03-18 03:46:23,565] [INFO] Total running time: 0h1m13s