[2023-03-17 00:26:56,230] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:26:56,230] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:26:56,230] [INFO] DQC Reference Directory: /var/lib/cwl/stg81bd5423-b2f9-4c76-813b-8f6b962945a8/dqc_reference
[2023-03-17 00:26:57,319] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:26:57,319] [INFO] Task started: Prodigal
[2023-03-17 00:26:57,319] [INFO] Running command: cat /var/lib/cwl/stg40379b0d-87a3-42f2-974d-f393d8fbf6db/OceanDNA-b30483.fa | prodigal -d OceanDNA-b30483/cds.fna -a OceanDNA-b30483/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:27:20,156] [INFO] Task succeeded: Prodigal
[2023-03-17 00:27:20,156] [INFO] Task started: HMMsearch
[2023-03-17 00:27:20,156] [INFO] Running command: hmmsearch --tblout OceanDNA-b30483/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81bd5423-b2f9-4c76-813b-8f6b962945a8/dqc_reference/reference_markers.hmm OceanDNA-b30483/protein.faa > /dev/null
[2023-03-17 00:27:20,356] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:27:20,357] [INFO] Found 6/6 markers.
[2023-03-17 00:27:20,380] [INFO] Query marker FASTA was written to OceanDNA-b30483/markers.fasta
[2023-03-17 00:27:20,381] [INFO] Task started: Blastn
[2023-03-17 00:27:20,381] [INFO] Running command: blastn -query OceanDNA-b30483/markers.fasta -db /var/lib/cwl/stg81bd5423-b2f9-4c76-813b-8f6b962945a8/dqc_reference/reference_markers.fasta -out OceanDNA-b30483/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:27:21,018] [INFO] Task succeeded: Blastn
[2023-03-17 00:27:21,020] [INFO] Selected 35 target genomes.
[2023-03-17 00:27:21,020] [INFO] Target genome list was writen to OceanDNA-b30483/target_genomes.txt
[2023-03-17 00:27:21,032] [INFO] Task started: fastANI
[2023-03-17 00:27:21,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg40379b0d-87a3-42f2-974d-f393d8fbf6db/OceanDNA-b30483.fa --refList OceanDNA-b30483/target_genomes.txt --output OceanDNA-b30483/fastani_result.tsv --threads 1
[2023-03-17 00:30:37,313] [INFO] Task succeeded: fastANI
[2023-03-17 00:30:37,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81bd5423-b2f9-4c76-813b-8f6b962945a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:30:37,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81bd5423-b2f9-4c76-813b-8f6b962945a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:30:37,332] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:30:37,332] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:30:37,333] [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
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	78.0357	374	1141	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	77.6823	371	1141	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.4334	332	1141	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.418	332	1141	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.0229	156	1141	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.012	245	1141	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.9922	200	1141	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	76.981	202	1141	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	76.9802	235	1141	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	76.9581	199	1141	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.9076	266	1141	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	76.9072	168	1141	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	76.9056	216	1141	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.8475	240	1141	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8036	164	1141	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.7941	104	1141	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.7409	242	1141	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	76.7081	219	1141	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	76.6957	220	1141	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.6646	209	1141	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.6331	214	1141	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.5848	181	1141	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	76.5653	199	1141	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.5649	98	1141	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	76.494	151	1141	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	76.4614	166	1141	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.4227	181	1141	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.419	205	1141	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.3006	192	1141	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	76.2578	126	1141	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.1712	156	1141	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	75.8484	94	1141	95	below_threshold
Pontibaca salina	strain=S1109L	GCA_016307205.1	2795731	2795731	type	True	75.8438	105	1141	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	75.6279	104	1141	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	75.4785	103	1141	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:30:37,333] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30483/tc_result.tsv
[2023-03-17 00:30:37,333] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:30:37,333] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:30:37,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81bd5423-b2f9-4c76-813b-8f6b962945a8/dqc_reference/checkm_data
[2023-03-17 00:30:37,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:30:37,341] [INFO] Task started: CheckM
[2023-03-17 00:30:37,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30483/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30483/checkm_input OceanDNA-b30483/checkm_result
[2023-03-17 00:31:35,339] [INFO] Task succeeded: CheckM
[2023-03-17 00:31:35,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:31:35,342] [INFO] ===== Completeness check finished =====
[2023-03-17 00:31:35,342] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:31:35,342] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30483/markers.fasta)
[2023-03-17 00:31:35,343] [INFO] Task started: Blastn
[2023-03-17 00:31:35,343] [INFO] Running command: blastn -query OceanDNA-b30483/markers.fasta -db /var/lib/cwl/stg81bd5423-b2f9-4c76-813b-8f6b962945a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30483/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:31:36,310] [INFO] Task succeeded: Blastn
[2023-03-17 00:31:36,311] [INFO] Selected 25 target genomes.
[2023-03-17 00:31:36,311] [INFO] Target genome list was writen to OceanDNA-b30483/target_genomes_gtdb.txt
[2023-03-17 00:31:36,376] [INFO] Task started: fastANI
[2023-03-17 00:31:36,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg40379b0d-87a3-42f2-974d-f393d8fbf6db/OceanDNA-b30483.fa --refList OceanDNA-b30483/target_genomes_gtdb.txt --output OceanDNA-b30483/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:31:54,253] [INFO] Task succeeded: fastANI
[2023-03-17 00:31:54,267] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:31:54,267] [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_900143535.1	s__Tateyamaria sp900143535	78.688	561	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	77.8472	461	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.8104	332	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995245.1	s__Tateyamaria sp007995245	77.6944	427	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651375.1	s__Tateyamaria omphalii	77.6762	371	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	77.597	428	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.516	304	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.4252	333	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.1402	261	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	77.0571	240	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	77.0554	154	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	76.9922	200	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018668195.1	s__Tateyamaria sp018668195	76.975	184	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	76.9492	199	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	76.8968	218	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065155.1	s__SW4 sp002732825	76.8744	183	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SW4	95.0	98.61	98.61	0.85	0.85	2	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.7495	241	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811755.1	s__Roseobacter cerasinus	76.7081	219	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441615.1	s__Roseovarius atlanticus	76.525	172	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	76.4861	178	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900182615.1	s__Ruegeria faecimaris	76.4768	152	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.4266	202	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_900115165.1	s__Roseovarius lutimaris	76.4227	181	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	76.2881	179	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	76.2298	128	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:31:54,267] [INFO] GTDB search result was written to OceanDNA-b30483/result_gtdb.tsv
[2023-03-17 00:31:54,267] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:31:54,270] [INFO] DFAST_QC result json was written to OceanDNA-b30483/dqc_result.json
[2023-03-17 00:31:54,270] [INFO] DFAST_QC completed!
[2023-03-17 00:31:54,271] [INFO] Total running time: 0h4m58s