[2023-03-16 16:56:57,619] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:56:57,619] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:56:57,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgd04406a5-226e-4c89-a37b-119e1356e3ec/dqc_reference
[2023-03-16 16:56:58,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:56:58,766] [INFO] Task started: Prodigal
[2023-03-16 16:56:58,767] [INFO] Running command: cat /var/lib/cwl/stgc62aee85-3645-49ae-be48-c46431f52074/OceanDNA-b28141.fa | prodigal -d OceanDNA-b28141/cds.fna -a OceanDNA-b28141/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:57:14,532] [INFO] Task succeeded: Prodigal
[2023-03-16 16:57:14,533] [INFO] Task started: HMMsearch
[2023-03-16 16:57:14,533] [INFO] Running command: hmmsearch --tblout OceanDNA-b28141/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd04406a5-226e-4c89-a37b-119e1356e3ec/dqc_reference/reference_markers.hmm OceanDNA-b28141/protein.faa > /dev/null
[2023-03-16 16:57:14,729] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:57:14,729] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc62aee85-3645-49ae-be48-c46431f52074/OceanDNA-b28141.fa]
[2023-03-16 16:57:14,750] [INFO] Query marker FASTA was written to OceanDNA-b28141/markers.fasta
[2023-03-16 16:57:14,751] [INFO] Task started: Blastn
[2023-03-16 16:57:14,751] [INFO] Running command: blastn -query OceanDNA-b28141/markers.fasta -db /var/lib/cwl/stgd04406a5-226e-4c89-a37b-119e1356e3ec/dqc_reference/reference_markers.fasta -out OceanDNA-b28141/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:57:15,332] [INFO] Task succeeded: Blastn
[2023-03-16 16:57:15,333] [INFO] Selected 28 target genomes.
[2023-03-16 16:57:15,333] [INFO] Target genome list was writen to OceanDNA-b28141/target_genomes.txt
[2023-03-16 16:57:15,351] [INFO] Task started: fastANI
[2023-03-16 16:57:15,351] [INFO] Running command: fastANI --query /var/lib/cwl/stgc62aee85-3645-49ae-be48-c46431f52074/OceanDNA-b28141.fa --refList OceanDNA-b28141/target_genomes.txt --output OceanDNA-b28141/fastani_result.tsv --threads 1
[2023-03-16 16:57:33,073] [INFO] Task succeeded: fastANI
[2023-03-16 16:57:33,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd04406a5-226e-4c89-a37b-119e1356e3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:57:33,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd04406a5-226e-4c89-a37b-119e1356e3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:57:33,088] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:57:33,088] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:57:33,088] [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
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	77.99	217	853	95	below_threshold
Cognatishimia maritima	strain=DSM 28223	GCA_900129685.1	870908	870908	type	True	77.8654	251	853	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	77.7058	204	853	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	77.6149	207	853	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.4853	197	853	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.4184	198	853	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.158	216	853	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	77.0644	180	853	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.9578	181	853	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	76.9397	149	853	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	76.7498	192	853	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	76.709	178	853	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.6965	94	853	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	76.6918	177	853	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	76.6685	181	853	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	76.6628	152	853	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.6502	126	853	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.5891	129	853	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.5538	149	853	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.5424	179	853	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.4584	109	853	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.3732	102	853	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	76.1233	115	853	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.0799	94	853	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.0685	91	853	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.0154	103	853	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	75.947	111	853	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	75.9342	112	853	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:57:33,089] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28141/tc_result.tsv
[2023-03-16 16:57:33,089] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:57:33,089] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:57:33,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd04406a5-226e-4c89-a37b-119e1356e3ec/dqc_reference/checkm_data
[2023-03-16 16:57:33,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:57:33,095] [INFO] Task started: CheckM
[2023-03-16 16:57:33,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28141/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28141/checkm_input OceanDNA-b28141/checkm_result
[2023-03-16 16:58:21,565] [INFO] Task succeeded: CheckM
[2023-03-16 16:58:21,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:58:21,569] [INFO] ===== Completeness check finished =====
[2023-03-16 16:58:21,569] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:58:21,569] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28141/markers.fasta)
[2023-03-16 16:58:21,571] [INFO] Task started: Blastn
[2023-03-16 16:58:21,571] [INFO] Running command: blastn -query OceanDNA-b28141/markers.fasta -db /var/lib/cwl/stgd04406a5-226e-4c89-a37b-119e1356e3ec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28141/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:58:23,675] [INFO] Task succeeded: Blastn
[2023-03-16 16:58:23,677] [INFO] Selected 20 target genomes.
[2023-03-16 16:58:23,677] [INFO] Target genome list was writen to OceanDNA-b28141/target_genomes_gtdb.txt
[2023-03-16 16:58:23,712] [INFO] Task started: fastANI
[2023-03-16 16:58:23,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgc62aee85-3645-49ae-be48-c46431f52074/OceanDNA-b28141.fa --refList OceanDNA-b28141/target_genomes_gtdb.txt --output OceanDNA-b28141/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:58:44,620] [INFO] Task succeeded: fastANI
[2023-03-16 16:58:44,631] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:58:44,632] [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_013215215.1	s__Cognatishimia sp013215215	81.0874	509	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798205.1	s__Cognatishimia activa_A	81.0297	545	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458335.1	s__Cognatishimia activa	77.99	217	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	99.97	99.97	0.99	0.99	2	-
GCF_900129685.1	s__Cognatishimia maritima	77.8654	251	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458175.1	s__Shimia marina	77.4706	198	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_017744095.1	s__Shimia sp017744095	77.4418	218	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	77.2621	195	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496005.1	s__Epibacterium litoralis	77.119	137	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	76.9448	182	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	76.8961	196	853	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_016888515.1	s__Shimia_A biformata	76.889	203	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018678075.1	s__Epibacterium ulvae_A	76.7763	151	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	76.7632	185	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_900302455.1	s__Ruegeria_E mediterranea	76.7509	191	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCF_000152625.1	s__Roseovarius nubinhibens	76.7011	147	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_001681715.1	s__Epibacterium mobile	76.6918	177	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	97.01	96.41	0.91	0.87	56	-
GCF_018219815.1	s__Thalassobius aquimarinus	76.5452	151	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	76.5424	179	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	76.5339	169	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123675.1	s__Leisingera sp004123675	76.5332	177	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-16 16:58:44,632] [INFO] GTDB search result was written to OceanDNA-b28141/result_gtdb.tsv
[2023-03-16 16:58:44,632] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:58:44,634] [INFO] DFAST_QC result json was written to OceanDNA-b28141/dqc_result.json
[2023-03-16 16:58:44,634] [INFO] DFAST_QC completed!
[2023-03-16 16:58:44,635] [INFO] Total running time: 0h1m47s