[2023-03-15 08:30:43,833] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:30:43,836] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:30:43,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg8dec0e39-ddf3-434e-8f75-ac29e24af222/dqc_reference
[2023-03-15 08:30:44,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:30:44,962] [INFO] Task started: Prodigal
[2023-03-15 08:30:44,962] [INFO] Running command: cat /var/lib/cwl/stg4b59929e-dff3-4ffc-ae09-5e7f17fbbd49/OceanDNA-b30082.fa | prodigal -d OceanDNA-b30082/cds.fna -a OceanDNA-b30082/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:31:00,854] [INFO] Task succeeded: Prodigal
[2023-03-15 08:31:00,854] [INFO] Task started: HMMsearch
[2023-03-15 08:31:00,854] [INFO] Running command: hmmsearch --tblout OceanDNA-b30082/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8dec0e39-ddf3-434e-8f75-ac29e24af222/dqc_reference/reference_markers.hmm OceanDNA-b30082/protein.faa > /dev/null
[2023-03-15 08:31:01,046] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:31:01,047] [INFO] Found 6/6 markers.
[2023-03-15 08:31:01,063] [INFO] Query marker FASTA was written to OceanDNA-b30082/markers.fasta
[2023-03-15 08:31:01,064] [INFO] Task started: Blastn
[2023-03-15 08:31:01,064] [INFO] Running command: blastn -query OceanDNA-b30082/markers.fasta -db /var/lib/cwl/stg8dec0e39-ddf3-434e-8f75-ac29e24af222/dqc_reference/reference_markers.fasta -out OceanDNA-b30082/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:31:01,803] [INFO] Task succeeded: Blastn
[2023-03-15 08:31:01,804] [INFO] Selected 27 target genomes.
[2023-03-15 08:31:01,805] [INFO] Target genome list was writen to OceanDNA-b30082/target_genomes.txt
[2023-03-15 08:31:01,816] [INFO] Task started: fastANI
[2023-03-15 08:31:01,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b59929e-dff3-4ffc-ae09-5e7f17fbbd49/OceanDNA-b30082.fa --refList OceanDNA-b30082/target_genomes.txt --output OceanDNA-b30082/fastani_result.tsv --threads 1
[2023-03-15 08:31:19,544] [INFO] Task succeeded: fastANI
[2023-03-15 08:31:19,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8dec0e39-ddf3-434e-8f75-ac29e24af222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:31:19,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8dec0e39-ddf3-434e-8f75-ac29e24af222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:31:19,559] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:31:19,559] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:31:19,560] [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
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.7813	419	815	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.2806	386	815	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	78.1117	357	815	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.0724	356	815	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	77.9933	398	815	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.8765	312	815	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	77.8741	349	815	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	77.8484	321	815	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	77.8122	292	815	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	77.6324	305	815	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	77.5052	288	815	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	77.4748	282	815	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.3732	268	815	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.3668	321	815	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.3602	279	815	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.3487	326	815	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	77.2129	210	815	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.1278	194	815	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.0304	222	815	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	76.9249	197	815	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.9221	180	815	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.9052	196	815	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8859	221	815	95	below_threshold
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	76.8702	141	815	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	76.7533	206	815	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.6182	176	815	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.3261	152	815	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:31:19,563] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30082/tc_result.tsv
[2023-03-15 08:31:19,564] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:31:19,564] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:31:19,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8dec0e39-ddf3-434e-8f75-ac29e24af222/dqc_reference/checkm_data
[2023-03-15 08:31:19,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:31:19,619] [INFO] Task started: CheckM
[2023-03-15 08:31:19,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30082/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30082/checkm_input OceanDNA-b30082/checkm_result
[2023-03-15 08:32:04,358] [INFO] Task succeeded: CheckM
[2023-03-15 08:32:04,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:32:04,411] [INFO] ===== Completeness check finished =====
[2023-03-15 08:32:04,411] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:32:04,412] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30082/markers.fasta)
[2023-03-15 08:32:04,412] [INFO] Task started: Blastn
[2023-03-15 08:32:04,413] [INFO] Running command: blastn -query OceanDNA-b30082/markers.fasta -db /var/lib/cwl/stg8dec0e39-ddf3-434e-8f75-ac29e24af222/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30082/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:32:05,767] [INFO] Task succeeded: Blastn
[2023-03-15 08:32:05,769] [INFO] Selected 16 target genomes.
[2023-03-15 08:32:05,769] [INFO] Target genome list was writen to OceanDNA-b30082/target_genomes_gtdb.txt
[2023-03-15 08:32:05,789] [INFO] Task started: fastANI
[2023-03-15 08:32:05,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b59929e-dff3-4ffc-ae09-5e7f17fbbd49/OceanDNA-b30082.fa --refList OceanDNA-b30082/target_genomes_gtdb.txt --output OceanDNA-b30082/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:32:17,896] [INFO] Task succeeded: fastANI
[2023-03-15 08:32:17,905] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:32:17,905] [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_003122245.1	s__Roseovarius sp003122245	86.9576	720	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	78.7806	419	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156535.1	s__Roseovarius nanhaiticus	78.687	391	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003651245.1	s__Roseovarius spongiae	78.3339	394	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	78.2725	388	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_003316635.1	s__Roseovarius dicentrarchi	78.1218	356	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172255.1	s__Roseovarius halotolerans	77.8687	319	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014359765.1	s__Roseovarius sp014359765	77.756	256	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109455.1	s__Roseovarius azorensis	77.6423	304	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	77.5664	336	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_006125015.1	s__Roseovarius arcticus	77.528	306	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172285.1	s__Roseovarius aestuarii	77.4574	281	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.3602	279	815	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_009789075.1	s__Pseudooceanicola pacificus	76.9367	182	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	76.9035	221	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	76.7533	206	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
--------------------------------------------------------------------------------
[2023-03-15 08:32:17,906] [INFO] GTDB search result was written to OceanDNA-b30082/result_gtdb.tsv
[2023-03-15 08:32:17,906] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:32:17,908] [INFO] DFAST_QC result json was written to OceanDNA-b30082/dqc_result.json
[2023-03-15 08:32:17,908] [INFO] DFAST_QC completed!
[2023-03-15 08:32:17,908] [INFO] Total running time: 0h1m34s