[2023-03-19 01:25:20,232] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:25:20,232] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:25:20,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg8548c993-41d3-4452-97f2-e1287d83424b/dqc_reference
[2023-03-19 01:25:21,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:25:21,340] [INFO] Task started: Prodigal
[2023-03-19 01:25:21,340] [INFO] Running command: cat /var/lib/cwl/stg5a8f8daa-7112-4be0-bcc1-a8c30b12f9bb/OceanDNA-b30174.fa | prodigal -d OceanDNA-b30174/cds.fna -a OceanDNA-b30174/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:25:44,633] [INFO] Task succeeded: Prodigal
[2023-03-19 01:25:44,633] [INFO] Task started: HMMsearch
[2023-03-19 01:25:44,633] [INFO] Running command: hmmsearch --tblout OceanDNA-b30174/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8548c993-41d3-4452-97f2-e1287d83424b/dqc_reference/reference_markers.hmm OceanDNA-b30174/protein.faa > /dev/null
[2023-03-19 01:25:44,840] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:25:44,841] [INFO] Found 6/6 markers.
[2023-03-19 01:25:44,865] [INFO] Query marker FASTA was written to OceanDNA-b30174/markers.fasta
[2023-03-19 01:25:44,866] [INFO] Task started: Blastn
[2023-03-19 01:25:44,866] [INFO] Running command: blastn -query OceanDNA-b30174/markers.fasta -db /var/lib/cwl/stg8548c993-41d3-4452-97f2-e1287d83424b/dqc_reference/reference_markers.fasta -out OceanDNA-b30174/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:25:45,558] [INFO] Task succeeded: Blastn
[2023-03-19 01:25:45,560] [INFO] Selected 21 target genomes.
[2023-03-19 01:25:45,560] [INFO] Target genome list was writen to OceanDNA-b30174/target_genomes.txt
[2023-03-19 01:25:45,575] [INFO] Task started: fastANI
[2023-03-19 01:25:45,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8f8daa-7112-4be0-bcc1-a8c30b12f9bb/OceanDNA-b30174.fa --refList OceanDNA-b30174/target_genomes.txt --output OceanDNA-b30174/fastani_result.tsv --threads 1
[2023-03-19 01:25:59,719] [INFO] Task succeeded: fastANI
[2023-03-19 01:25:59,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8548c993-41d3-4452-97f2-e1287d83424b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:25:59,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8548c993-41d3-4452-97f2-e1287d83424b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:25:59,732] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:25:59,732] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:25:59,732] [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
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.5877	521	1188	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	78.5071	532	1188	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	78.1874	432	1188	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	78.1735	438	1188	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	78.1417	484	1188	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.9448	368	1188	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	77.4729	282	1188	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.4513	338	1188	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.4402	339	1188	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.3949	330	1188	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.3526	335	1188	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.6417	193	1188	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.63	187	1188	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.5725	228	1188	95	below_threshold
Donghicola mangrovi	strain=B5-SW-15	GCA_013377535.1	2729614	2729614	type	True	76.5268	143	1188	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	76.3646	145	1188	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	76.2994	195	1188	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.1172	106	1188	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	75.6637	88	1188	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	75.4602	74	1188	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.3354	51	1188	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:25:59,733] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30174/tc_result.tsv
[2023-03-19 01:25:59,734] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:25:59,734] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:25:59,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8548c993-41d3-4452-97f2-e1287d83424b/dqc_reference/checkm_data
[2023-03-19 01:25:59,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:25:59,741] [INFO] Task started: CheckM
[2023-03-19 01:25:59,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30174/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30174/checkm_input OceanDNA-b30174/checkm_result
[2023-03-19 01:26:57,979] [INFO] Task succeeded: CheckM
[2023-03-19 01:26:57,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:26:58,170] [INFO] ===== Completeness check finished =====
[2023-03-19 01:26:58,170] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:26:58,170] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30174/markers.fasta)
[2023-03-19 01:26:58,171] [INFO] Task started: Blastn
[2023-03-19 01:26:58,172] [INFO] Running command: blastn -query OceanDNA-b30174/markers.fasta -db /var/lib/cwl/stg8548c993-41d3-4452-97f2-e1287d83424b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30174/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:26:59,351] [INFO] Task succeeded: Blastn
[2023-03-19 01:26:59,352] [INFO] Selected 18 target genomes.
[2023-03-19 01:26:59,352] [INFO] Target genome list was writen to OceanDNA-b30174/target_genomes_gtdb.txt
[2023-03-19 01:26:59,374] [INFO] Task started: fastANI
[2023-03-19 01:26:59,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8f8daa-7112-4be0-bcc1-a8c30b12f9bb/OceanDNA-b30174.fa --refList OceanDNA-b30174/target_genomes_gtdb.txt --output OceanDNA-b30174/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:27:13,838] [INFO] Task succeeded: fastANI
[2023-03-19 01:27:13,849] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:27:13,849] [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_017854675.1	s__Sulfitobacter sp017854675	96.1235	913	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017854855.1	s__Sulfitobacter sp017854855	78.6955	530	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	78.5148	531	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	78.2392	459	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	78.2093	517	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	78.1857	436	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000622365.1	s__Sulfitobacter noctilucae	78.1492	483	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	78.0645	437	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_001650875.1	s__Sulfitobacter sp001650875	78.0056	481	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	77.9052	476	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.7015	414	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.6435	314	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.5933	384	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	77.5426	371	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196805.1	s__Sulfitobacter undariae	77.4837	281	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172095.1	s__Sulfitobacter indolifex	77.3949	330	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.2662	351	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003352085.1	s__Sulfitobacter sp003352085	77.2048	306	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:27:13,850] [INFO] GTDB search result was written to OceanDNA-b30174/result_gtdb.tsv
[2023-03-19 01:27:13,850] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:27:13,852] [INFO] DFAST_QC result json was written to OceanDNA-b30174/dqc_result.json
[2023-03-19 01:27:13,852] [INFO] DFAST_QC completed!
[2023-03-19 01:27:13,852] [INFO] Total running time: 0h1m54s