[2023-03-18 21:08:05,358] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:08:05,359] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:08:05,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0e695ee-3a80-4741-99c6-7fe6ae80261f/dqc_reference
[2023-03-18 21:08:06,465] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:08:06,466] [INFO] Task started: Prodigal
[2023-03-18 21:08:06,466] [INFO] Running command: cat /var/lib/cwl/stg7ef427bd-1f7e-421b-a7ea-b0e10c47f87a/OceanDNA-b28545.fa | prodigal -d OceanDNA-b28545/cds.fna -a OceanDNA-b28545/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:08:27,409] [INFO] Task succeeded: Prodigal
[2023-03-18 21:08:27,410] [INFO] Task started: HMMsearch
[2023-03-18 21:08:27,410] [INFO] Running command: hmmsearch --tblout OceanDNA-b28545/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0e695ee-3a80-4741-99c6-7fe6ae80261f/dqc_reference/reference_markers.hmm OceanDNA-b28545/protein.faa > /dev/null
[2023-03-18 21:08:27,597] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:08:27,597] [INFO] Found 6/6 markers.
[2023-03-18 21:08:27,617] [INFO] Query marker FASTA was written to OceanDNA-b28545/markers.fasta
[2023-03-18 21:08:27,617] [INFO] Task started: Blastn
[2023-03-18 21:08:27,617] [INFO] Running command: blastn -query OceanDNA-b28545/markers.fasta -db /var/lib/cwl/stgd0e695ee-3a80-4741-99c6-7fe6ae80261f/dqc_reference/reference_markers.fasta -out OceanDNA-b28545/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:08:28,413] [INFO] Task succeeded: Blastn
[2023-03-18 21:08:28,414] [INFO] Selected 29 target genomes.
[2023-03-18 21:08:28,414] [INFO] Target genome list was writen to OceanDNA-b28545/target_genomes.txt
[2023-03-18 21:08:28,424] [INFO] Task started: fastANI
[2023-03-18 21:08:28,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ef427bd-1f7e-421b-a7ea-b0e10c47f87a/OceanDNA-b28545.fa --refList OceanDNA-b28545/target_genomes.txt --output OceanDNA-b28545/fastani_result.tsv --threads 1
[2023-03-18 21:08:47,852] [INFO] Task succeeded: fastANI
[2023-03-18 21:08:47,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0e695ee-3a80-4741-99c6-7fe6ae80261f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:08:47,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0e695ee-3a80-4741-99c6-7fe6ae80261f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:08:47,868] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:08:47,868] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:08:47,868] [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
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	78.5881	284	1090	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	78.5575	288	1090	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	78.3772	366	1090	95	below_threshold
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	78.2875	339	1090	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	78.1241	337	1090	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	78.0477	276	1090	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.0197	269	1090	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.9722	327	1090	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.7888	367	1090	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.4723	253	1090	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	77.4007	298	1090	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.3982	296	1090	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	77.3956	272	1090	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	77.3565	233	1090	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.2883	232	1090	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	77.2266	283	1090	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	77.2236	277	1090	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.2164	291	1090	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.2114	298	1090	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.2026	279	1090	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.1284	277	1090	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.0391	261	1090	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.9531	203	1090	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.9281	250	1090	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	76.7946	202	1090	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	76.7614	216	1090	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	76.7468	205	1090	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.693	246	1090	95	below_threshold
Albidovulum inexpectatum	strain=DSM 12048	GCA_002927635.1	196587	196587	type	True	76.6906	206	1090	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:08:47,868] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28545/tc_result.tsv
[2023-03-18 21:08:47,868] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:08:47,868] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:08:47,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0e695ee-3a80-4741-99c6-7fe6ae80261f/dqc_reference/checkm_data
[2023-03-18 21:08:47,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:08:47,936] [INFO] Task started: CheckM
[2023-03-18 21:08:47,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28545/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28545/checkm_input OceanDNA-b28545/checkm_result
[2023-03-18 21:09:40,650] [INFO] Task succeeded: CheckM
[2023-03-18 21:09:40,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:09:40,654] [INFO] ===== Completeness check finished =====
[2023-03-18 21:09:40,654] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:09:40,654] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28545/markers.fasta)
[2023-03-18 21:09:40,655] [INFO] Task started: Blastn
[2023-03-18 21:09:40,655] [INFO] Running command: blastn -query OceanDNA-b28545/markers.fasta -db /var/lib/cwl/stgd0e695ee-3a80-4741-99c6-7fe6ae80261f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28545/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:09:42,115] [INFO] Task succeeded: Blastn
[2023-03-18 21:09:42,116] [INFO] Selected 23 target genomes.
[2023-03-18 21:09:42,116] [INFO] Target genome list was writen to OceanDNA-b28545/target_genomes_gtdb.txt
[2023-03-18 21:09:42,141] [INFO] Task started: fastANI
[2023-03-18 21:09:42,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ef427bd-1f7e-421b-a7ea-b0e10c47f87a/OceanDNA-b28545.fa --refList OceanDNA-b28545/target_genomes_gtdb.txt --output OceanDNA-b28545/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:09:57,909] [INFO] Task succeeded: fastANI
[2023-03-18 21:09:57,921] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:09:57,922] [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_002706605.1	s__SAT37 sp002706605	99.9957	1082	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	conclusive
GCF_002285435.1	s__Actibacterium ureilyticum	78.6417	460	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	78.5589	286	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000671395.1	s__Actibacterium atlanticum	78.3735	367	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.9887	351	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.8062	365	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.7614	370	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278325.1	s__JADQCB01 sp016278325	77.6111	281	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	77.5367	356	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002079305.1	s__Rhodovulum sp002079305	77.52	304	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	77.4741	290	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112245.1	s__Ruegeria sp013112245	77.4433	222	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.18	96.94	0.93	0.89	11	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	77.423	308	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030265.1	s__Ruegeria arenilitoris_E	77.4057	194	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002504165.1	s__Pacificitalea manganoxidans	77.3956	272	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	77.3565	233	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_000813725.1	s__Leisingera sp000813725	77.2441	248	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	77.2359	283	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004339675.1	s__Rhodovulum steppense	77.2072	292	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	77.1729	250	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	76.9381	249	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278285.1	s__JADQCB01 sp016278285	76.8067	216	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	76.7476	205	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
--------------------------------------------------------------------------------
[2023-03-18 21:09:57,922] [INFO] GTDB search result was written to OceanDNA-b28545/result_gtdb.tsv
[2023-03-18 21:09:57,923] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:09:57,926] [INFO] DFAST_QC result json was written to OceanDNA-b28545/dqc_result.json
[2023-03-18 21:09:57,926] [INFO] DFAST_QC completed!
[2023-03-18 21:09:57,926] [INFO] Total running time: 0h1m53s