[2023-03-15 15:56:48,659] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:56:48,660] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:56:48,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ddb66c6-cb76-4c4f-9b6f-f5e47de0ee2d/dqc_reference
[2023-03-15 15:56:49,759] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:56:49,759] [INFO] Task started: Prodigal
[2023-03-15 15:56:49,759] [INFO] Running command: cat /var/lib/cwl/stgac687559-2956-427e-affb-55d55df590de/OceanDNA-b30235.fa | prodigal -d OceanDNA-b30235/cds.fna -a OceanDNA-b30235/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:57:11,826] [INFO] Task succeeded: Prodigal
[2023-03-15 15:57:11,827] [INFO] Task started: HMMsearch
[2023-03-15 15:57:11,827] [INFO] Running command: hmmsearch --tblout OceanDNA-b30235/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ddb66c6-cb76-4c4f-9b6f-f5e47de0ee2d/dqc_reference/reference_markers.hmm OceanDNA-b30235/protein.faa > /dev/null
[2023-03-15 15:57:12,031] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:57:12,032] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgac687559-2956-427e-affb-55d55df590de/OceanDNA-b30235.fa]
[2023-03-15 15:57:12,061] [INFO] Query marker FASTA was written to OceanDNA-b30235/markers.fasta
[2023-03-15 15:57:12,061] [INFO] Task started: Blastn
[2023-03-15 15:57:12,061] [INFO] Running command: blastn -query OceanDNA-b30235/markers.fasta -db /var/lib/cwl/stg1ddb66c6-cb76-4c4f-9b6f-f5e47de0ee2d/dqc_reference/reference_markers.fasta -out OceanDNA-b30235/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:57:12,684] [INFO] Task succeeded: Blastn
[2023-03-15 15:57:12,685] [INFO] Selected 22 target genomes.
[2023-03-15 15:57:12,685] [INFO] Target genome list was writen to OceanDNA-b30235/target_genomes.txt
[2023-03-15 15:57:12,753] [INFO] Task started: fastANI
[2023-03-15 15:57:12,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgac687559-2956-427e-affb-55d55df590de/OceanDNA-b30235.fa --refList OceanDNA-b30235/target_genomes.txt --output OceanDNA-b30235/fastani_result.tsv --threads 1
[2023-03-15 15:57:26,629] [INFO] Task succeeded: fastANI
[2023-03-15 15:57:26,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ddb66c6-cb76-4c4f-9b6f-f5e47de0ee2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:57:26,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ddb66c6-cb76-4c4f-9b6f-f5e47de0ee2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:57:26,641] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:57:26,641] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:57:26,641] [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 brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	77.5222	264	1146	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.2538	281	1146	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.1602	263	1146	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.1506	210	1146	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.1371	263	1146	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.0945	244	1146	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.0894	231	1146	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.0858	262	1146	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.0665	231	1146	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	76.9814	212	1146	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	76.9034	232	1146	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.8869	197	1146	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.8563	194	1146	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	76.8184	196	1146	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.7777	159	1146	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.7629	158	1146	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.661	160	1146	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.4382	169	1146	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.3403	155	1146	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	76.096	119	1146	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	76.0184	99	1146	95	below_threshold
Donghicola mangrovi	strain=B5-SW-15	GCA_013377535.1	2729614	2729614	type	True	75.7206	87	1146	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:57:26,642] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30235/tc_result.tsv
[2023-03-15 15:57:26,642] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:57:26,642] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:57:26,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ddb66c6-cb76-4c4f-9b6f-f5e47de0ee2d/dqc_reference/checkm_data
[2023-03-15 15:57:26,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:57:26,649] [INFO] Task started: CheckM
[2023-03-15 15:57:26,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30235/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30235/checkm_input OceanDNA-b30235/checkm_result
[2023-03-15 15:58:23,074] [INFO] Task succeeded: CheckM
[2023-03-15 15:58:23,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.16%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:58:23,078] [INFO] ===== Completeness check finished =====
[2023-03-15 15:58:23,078] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:58:23,079] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30235/markers.fasta)
[2023-03-15 15:58:23,080] [INFO] Task started: Blastn
[2023-03-15 15:58:23,080] [INFO] Running command: blastn -query OceanDNA-b30235/markers.fasta -db /var/lib/cwl/stg1ddb66c6-cb76-4c4f-9b6f-f5e47de0ee2d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30235/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:58:24,028] [INFO] Task succeeded: Blastn
[2023-03-15 15:58:24,030] [INFO] Selected 20 target genomes.
[2023-03-15 15:58:24,030] [INFO] Target genome list was writen to OceanDNA-b30235/target_genomes_gtdb.txt
[2023-03-15 15:58:24,048] [INFO] Task started: fastANI
[2023-03-15 15:58:24,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgac687559-2956-427e-affb-55d55df590de/OceanDNA-b30235.fa --refList OceanDNA-b30235/target_genomes_gtdb.txt --output OceanDNA-b30235/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:58:37,954] [INFO] Task succeeded: fastANI
[2023-03-15 15:58:37,966] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:58:37,966] [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_001650875.1	s__Sulfitobacter sp001650875	77.7886	295	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	77.6659	266	1146	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	77.5299	254	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112755.1	s__Sulfitobacter brevis	77.5222	264	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	77.5221	264	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	77.4697	335	1146	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	77.3071	269	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.2905	258	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.2437	282	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.1602	263	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.1053	243	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.0665	231	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_900103185.1	s__Sulfitobacter litoralis	76.9696	213	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_000622365.1	s__Sulfitobacter noctilucae	76.9027	232	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	76.8563	194	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000622405.1	s__Sulfitobacter donghicola	76.7777	159	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.661	160	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318255.1	s__Ruegeria sp003318255	76.4917	114	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458295.1	s__Ruegeria denitrificans	76.096	119	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377535.1	s__Donghicola mangrovi	75.7206	87	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	96.45	96.45	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:58:37,966] [INFO] GTDB search result was written to OceanDNA-b30235/result_gtdb.tsv
[2023-03-15 15:58:37,967] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:58:37,969] [INFO] DFAST_QC result json was written to OceanDNA-b30235/dqc_result.json
[2023-03-15 15:58:37,969] [INFO] DFAST_QC completed!
[2023-03-15 15:58:37,969] [INFO] Total running time: 0h1m49s