[2023-03-15 12:06:59,561] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:06:59,562] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:06:59,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd6aab4c-a07a-4f99-b0cf-761e533c48eb/dqc_reference
[2023-03-15 12:07:00,690] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:07:00,690] [INFO] Task started: Prodigal
[2023-03-15 12:07:00,691] [INFO] Running command: cat /var/lib/cwl/stgd321878f-c2fe-44a2-a7b4-906c9734e071/OceanDNA-b27612.fa | prodigal -d OceanDNA-b27612/cds.fna -a OceanDNA-b27612/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:07:18,061] [INFO] Task succeeded: Prodigal
[2023-03-15 12:07:18,062] [INFO] Task started: HMMsearch
[2023-03-15 12:07:18,062] [INFO] Running command: hmmsearch --tblout OceanDNA-b27612/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd6aab4c-a07a-4f99-b0cf-761e533c48eb/dqc_reference/reference_markers.hmm OceanDNA-b27612/protein.faa > /dev/null
[2023-03-15 12:07:18,249] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:07:18,249] [INFO] Found 6/6 markers.
[2023-03-15 12:07:18,269] [INFO] Query marker FASTA was written to OceanDNA-b27612/markers.fasta
[2023-03-15 12:07:18,270] [INFO] Task started: Blastn
[2023-03-15 12:07:18,270] [INFO] Running command: blastn -query OceanDNA-b27612/markers.fasta -db /var/lib/cwl/stgdd6aab4c-a07a-4f99-b0cf-761e533c48eb/dqc_reference/reference_markers.fasta -out OceanDNA-b27612/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:07:19,053] [INFO] Task succeeded: Blastn
[2023-03-15 12:07:19,055] [INFO] Selected 31 target genomes.
[2023-03-15 12:07:19,055] [INFO] Target genome list was writen to OceanDNA-b27612/target_genomes.txt
[2023-03-15 12:07:19,069] [INFO] Task started: fastANI
[2023-03-15 12:07:19,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgd321878f-c2fe-44a2-a7b4-906c9734e071/OceanDNA-b27612.fa --refList OceanDNA-b27612/target_genomes.txt --output OceanDNA-b27612/fastani_result.tsv --threads 1
[2023-03-15 12:07:38,132] [INFO] Task succeeded: fastANI
[2023-03-15 12:07:38,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd6aab4c-a07a-4f99-b0cf-761e533c48eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:07:38,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd6aab4c-a07a-4f99-b0cf-761e533c48eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:07:38,148] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:07:38,149] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:07:38,149] [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
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.0783	300	886	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.0317	306	886	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.9847	195	886	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.9804	294	886	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.9575	203	886	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.8067	326	886	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.7528	262	886	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.7235	292	886	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.6607	288	886	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.637	277	886	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.5683	228	886	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	77.5669	231	886	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.5433	250	886	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	77.509	209	886	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.4389	216	886	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.418	292	886	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.2651	191	886	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.238	191	886	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2353	199	886	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.2072	191	886	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	77.203	175	886	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.1934	192	886	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.1324	192	886	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	77.1233	195	886	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	77.1067	196	886	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	76.9701	109	886	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	76.7688	127	886	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.7437	163	886	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.7018	132	886	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.6753	129	886	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.5665	165	886	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:07:38,149] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27612/tc_result.tsv
[2023-03-15 12:07:38,149] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:07:38,150] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:07:38,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd6aab4c-a07a-4f99-b0cf-761e533c48eb/dqc_reference/checkm_data
[2023-03-15 12:07:38,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:07:38,156] [INFO] Task started: CheckM
[2023-03-15 12:07:38,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27612/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27612/checkm_input OceanDNA-b27612/checkm_result
[2023-03-15 12:08:25,860] [INFO] Task succeeded: CheckM
[2023-03-15 12:08:25,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.36%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 12:08:25,874] [INFO] ===== Completeness check finished =====
[2023-03-15 12:08:25,874] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:08:25,874] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27612/markers.fasta)
[2023-03-15 12:08:25,875] [INFO] Task started: Blastn
[2023-03-15 12:08:25,875] [INFO] Running command: blastn -query OceanDNA-b27612/markers.fasta -db /var/lib/cwl/stgdd6aab4c-a07a-4f99-b0cf-761e533c48eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27612/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:08:27,320] [INFO] Task succeeded: Blastn
[2023-03-15 12:08:27,325] [INFO] Selected 33 target genomes.
[2023-03-15 12:08:27,325] [INFO] Target genome list was writen to OceanDNA-b27612/target_genomes_gtdb.txt
[2023-03-15 12:08:27,450] [INFO] Task started: fastANI
[2023-03-15 12:08:27,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgd321878f-c2fe-44a2-a7b4-906c9734e071/OceanDNA-b27612.fa --refList OceanDNA-b27612/target_genomes_gtdb.txt --output OceanDNA-b27612/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:08:52,523] [INFO] Task succeeded: fastANI
[2023-03-15 12:08:52,541] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:08:52,541] [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_004358185.1	s__Antarcticimicrobium luteum	78.0206	307	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.9686	295	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	77.9575	203	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018401465.1	s__Aestuariivita sp018401465	77.897	313	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.87	297	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900129345.1	s__Ruegeria intermedia	77.8039	290	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.7962	327	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_013031405.1	s__Ruegeria sp013031405	77.6703	291	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	77.6607	288	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	77.5778	293	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	77.5357	273	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	77.5191	231	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441615.1	s__Roseovarius atlanticus	77.5069	210	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	77.4817	224	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	77.4429	232	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804335.1	s__Pelagimonas sp004804335	77.4389	207	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860705.1	s__Salipiger sp018860705	77.4295	212	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	77.418	292	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	77.3321	262	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.3034	255	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_002786295.1	s__Pseudooceanicola marinus	77.2929	189	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001679925.1	s__Leisingera sp001679925	77.2524	242	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003646465.1	s__Chachezhania antarctica	77.2161	218	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	77.195	256	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_004216475.1	s__GCA-004216475 sp004216475	77.1894	246	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743975.1	s__Ruegeria sp017743975	77.1643	205	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	77.0628	225	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813985.1	s__Ruegeria sp000813985	77.0381	191	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.0063	184	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346865.1	s__Shimia isoporae	76.9701	109	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.9325	162	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014065.1	s__Epibacterium sp000014065	76.9259	193	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	76.8721	186	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:08:52,544] [INFO] GTDB search result was written to OceanDNA-b27612/result_gtdb.tsv
[2023-03-15 12:08:52,547] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:08:52,553] [INFO] DFAST_QC result json was written to OceanDNA-b27612/dqc_result.json
[2023-03-15 12:08:52,553] [INFO] DFAST_QC completed!
[2023-03-15 12:08:52,553] [INFO] Total running time: 0h1m53s