[2023-03-15 22:06:34,748] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:06:34,749] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:06:34,749] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfb481c7-7084-4f23-8d5b-3d60c8e38a00/dqc_reference
[2023-03-15 22:06:35,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:06:35,885] [INFO] Task started: Prodigal
[2023-03-15 22:06:35,885] [INFO] Running command: cat /var/lib/cwl/stgc5622c83-4bab-44a5-855c-97a48fa983be/OceanDNA-b23843.fa | prodigal -d OceanDNA-b23843/cds.fna -a OceanDNA-b23843/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:06:54,630] [INFO] Task succeeded: Prodigal
[2023-03-15 22:06:54,630] [INFO] Task started: HMMsearch
[2023-03-15 22:06:54,631] [INFO] Running command: hmmsearch --tblout OceanDNA-b23843/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfb481c7-7084-4f23-8d5b-3d60c8e38a00/dqc_reference/reference_markers.hmm OceanDNA-b23843/protein.faa > /dev/null
[2023-03-15 22:06:54,817] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:06:54,817] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc5622c83-4bab-44a5-855c-97a48fa983be/OceanDNA-b23843.fa]
[2023-03-15 22:06:54,835] [INFO] Query marker FASTA was written to OceanDNA-b23843/markers.fasta
[2023-03-15 22:06:54,836] [INFO] Task started: Blastn
[2023-03-15 22:06:54,836] [INFO] Running command: blastn -query OceanDNA-b23843/markers.fasta -db /var/lib/cwl/stgbfb481c7-7084-4f23-8d5b-3d60c8e38a00/dqc_reference/reference_markers.fasta -out OceanDNA-b23843/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:06:55,545] [INFO] Task succeeded: Blastn
[2023-03-15 22:06:55,546] [INFO] Selected 27 target genomes.
[2023-03-15 22:06:55,546] [INFO] Target genome list was writen to OceanDNA-b23843/target_genomes.txt
[2023-03-15 22:06:55,586] [INFO] Task started: fastANI
[2023-03-15 22:06:55,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5622c83-4bab-44a5-855c-97a48fa983be/OceanDNA-b23843.fa --refList OceanDNA-b23843/target_genomes.txt --output OceanDNA-b23843/fastani_result.tsv --threads 1
[2023-03-15 22:07:12,391] [INFO] Task succeeded: fastANI
[2023-03-15 22:07:12,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfb481c7-7084-4f23-8d5b-3d60c8e38a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:07:12,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfb481c7-7084-4f23-8d5b-3d60c8e38a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:07:12,406] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:07:12,406] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:07:12,406] [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
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.2267	107	944	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	76.1998	66	944	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	76.1599	53	944	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.1501	114	944	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	76.1441	68	944	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	76.0949	70	944	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.048	83	944	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	76.0199	87	944	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	75.9959	90	944	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	75.9805	91	944	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	75.9573	117	944	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	75.939	95	944	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	75.9082	115	944	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	75.8772	116	944	95	below_threshold
Algimonas arctica	strain=KCTC 32513	GCA_014652695.1	1479486	1479486	type	True	75.874	85	944	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	75.8068	74	944	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	75.7878	98	944	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.7663	115	944	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	75.6643	61	944	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	75.5911	50	944	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	75.5856	76	944	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	75.563	79	944	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	75.5338	89	944	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.5196	79	944	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.4865	97	944	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:07:12,411] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23843/tc_result.tsv
[2023-03-15 22:07:12,413] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:07:12,413] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:07:12,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfb481c7-7084-4f23-8d5b-3d60c8e38a00/dqc_reference/checkm_data
[2023-03-15 22:07:12,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:07:12,423] [INFO] Task started: CheckM
[2023-03-15 22:07:12,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23843/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23843/checkm_input OceanDNA-b23843/checkm_result
[2023-03-15 22:07:59,888] [INFO] Task succeeded: CheckM
[2023-03-15 22:07:59,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:07:59,952] [INFO] ===== Completeness check finished =====
[2023-03-15 22:07:59,953] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:07:59,953] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23843/markers.fasta)
[2023-03-15 22:07:59,954] [INFO] Task started: Blastn
[2023-03-15 22:07:59,954] [INFO] Running command: blastn -query OceanDNA-b23843/markers.fasta -db /var/lib/cwl/stgbfb481c7-7084-4f23-8d5b-3d60c8e38a00/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23843/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:08:01,206] [INFO] Task succeeded: Blastn
[2023-03-15 22:08:01,223] [INFO] Selected 29 target genomes.
[2023-03-15 22:08:01,223] [INFO] Target genome list was writen to OceanDNA-b23843/target_genomes_gtdb.txt
[2023-03-15 22:08:01,342] [INFO] Task started: fastANI
[2023-03-15 22:08:01,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5622c83-4bab-44a5-855c-97a48fa983be/OceanDNA-b23843.fa --refList OceanDNA-b23843/target_genomes_gtdb.txt --output OceanDNA-b23843/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:08:20,486] [INFO] Task succeeded: fastANI
[2023-03-15 22:08:20,500] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:08:20,500] [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_000152745.1	s__Oceanicaulis sp000152745	76.302	78	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_011762095.1	s__Parvibaculum indicum	76.1599	53	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467375.1	s__Caulobacter sp016467375	76.1204	97	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793635.1	s__Marinicauda pacifica	76.0949	70	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_008630495.1	s__Oceanicaulis satelles	76.0693	105	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350535.1	s__Microvirga subterranea	76.0549	69	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001449105.1	s__Caulobacter vibrioides_C	76.0002	126	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201415.1	s__Chelatococcus_A composti	75.9805	91	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCF_016135805.1	s__Caulobacter hibisci	75.9573	117	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114375.1	s__Methylobacterium salsuginis	75.9542	94	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	75.9261	122	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCF_014652695.1	s__Litorimonas arctica	75.874	85	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643585.1	s__Maricaulis sp017643585	75.8598	54	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.94	99.90	0.97	0.94	3	-
GCF_003046175.1	s__Bosea sp003046175	75.813	77	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199935.1	s__Methylobacterium rhodinum	75.8006	97	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	75.7637	115	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_014642635.1	s__Aureimonas_A endophytica	75.7349	79	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176975.1	s__Aureimonas_A psammosilene	75.694	79	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	75.6744	87	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	75.6717	84	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425465.1	s__Methylobacterium sp001425465	75.6238	101	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	75.5448	96	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.4974	93	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	75.4865	97	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167455.1	s__Reyranella aerosaccus	75.485	56	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	75.2152	76	944	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:08:20,510] [INFO] GTDB search result was written to OceanDNA-b23843/result_gtdb.tsv
[2023-03-15 22:08:20,525] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:08:20,533] [INFO] DFAST_QC result json was written to OceanDNA-b23843/dqc_result.json
[2023-03-15 22:08:20,533] [INFO] DFAST_QC completed!
[2023-03-15 22:08:20,533] [INFO] Total running time: 0h1m46s