[2023-03-14 11:14:12,763] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,763] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg033d8446-aa54-4829-b39a-347fbd0bd803/dqc_reference
[2023-03-14 11:14:14,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,203] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,203] [INFO] Running command: cat /var/lib/cwl/stg5def3333-a462-4664-95af-ccfdf5c9b365/OceanDNA-b40232.fa | prodigal -d OceanDNA-b40232/cds.fna -a OceanDNA-b40232/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:35,760] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:35,761] [INFO] Task started: HMMsearch
[2023-03-14 11:14:35,761] [INFO] Running command: hmmsearch --tblout OceanDNA-b40232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg033d8446-aa54-4829-b39a-347fbd0bd803/dqc_reference/reference_markers.hmm OceanDNA-b40232/protein.faa > /dev/null
[2023-03-14 11:14:36,019] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:36,019] [INFO] Found 6/6 markers.
[2023-03-14 11:14:36,043] [INFO] Query marker FASTA was written to OceanDNA-b40232/markers.fasta
[2023-03-14 11:14:36,045] [INFO] Task started: Blastn
[2023-03-14 11:14:36,045] [INFO] Running command: blastn -query OceanDNA-b40232/markers.fasta -db /var/lib/cwl/stg033d8446-aa54-4829-b39a-347fbd0bd803/dqc_reference/reference_markers.fasta -out OceanDNA-b40232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:36,736] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:36,737] [INFO] Selected 35 target genomes.
[2023-03-14 11:14:36,738] [INFO] Target genome list was writen to OceanDNA-b40232/target_genomes.txt
[2023-03-14 11:14:36,763] [INFO] Task started: fastANI
[2023-03-14 11:14:36,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg5def3333-a462-4664-95af-ccfdf5c9b365/OceanDNA-b40232.fa --refList OceanDNA-b40232/target_genomes.txt --output OceanDNA-b40232/fastani_result.tsv --threads 1
[2023-03-14 11:14:59,182] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:59,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg033d8446-aa54-4829-b39a-347fbd0bd803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:59,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg033d8446-aa54-4829-b39a-347fbd0bd803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:59,195] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:59,195] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:59,195] [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
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.2028	81	1122	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.1784	70	1122	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	76.1503	58	1122	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	76.1283	68	1122	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.1068	74	1122	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.0962	51	1122	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.0573	51	1122	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.0343	77	1122	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.0055	51	1122	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	75.9952	66	1122	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	75.994	52	1122	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	75.9908	50	1122	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.9801	71	1122	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	75.9679	66	1122	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	75.953	61	1122	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	75.9189	88	1122	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.9064	58	1122	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	75.9049	89	1122	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	75.8966	54	1122	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	75.4959	60	1122	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	75.378	52	1122	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:59,196] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40232/tc_result.tsv
[2023-03-14 11:14:59,196] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:59,196] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:59,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg033d8446-aa54-4829-b39a-347fbd0bd803/dqc_reference/checkm_data
[2023-03-14 11:14:59,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:59,289] [INFO] Task started: CheckM
[2023-03-14 11:14:59,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40232/checkm_input OceanDNA-b40232/checkm_result
[2023-03-14 11:15:54,117] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:54,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:54,120] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:54,120] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:54,120] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40232/markers.fasta)
[2023-03-14 11:15:54,121] [INFO] Task started: Blastn
[2023-03-14 11:15:54,121] [INFO] Running command: blastn -query OceanDNA-b40232/markers.fasta -db /var/lib/cwl/stg033d8446-aa54-4829-b39a-347fbd0bd803/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:55,296] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:55,297] [INFO] Selected 34 target genomes.
[2023-03-14 11:15:55,297] [INFO] Target genome list was writen to OceanDNA-b40232/target_genomes_gtdb.txt
[2023-03-14 11:15:55,372] [INFO] Task started: fastANI
[2023-03-14 11:15:55,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg5def3333-a462-4664-95af-ccfdf5c9b365/OceanDNA-b40232.fa --refList OceanDNA-b40232/target_genomes_gtdb.txt --output OceanDNA-b40232/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:16:14,314] [INFO] Task succeeded: fastANI
[2023-03-14 11:16:14,325] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:16:14,325] [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_003556835.1	s__PWQG01 sp003556835	76.874	81	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__PWQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009844085.1	s__UBA9145 sp009844085	76.5132	91	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.17	97.62	0.91	0.85	13	-
GCF_000380335.1	s__Azotobacter vinelandii	76.2853	60	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	76.1283	68	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	76.1211	52	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015992245.1	s__Halomonas sp015992245	76.0801	51	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCA_002477465.1	s__UBA9145 sp002477465	76.0687	61	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	76.0578	65	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_900100535.1	s__Pseudomonas_E flavescens	76.0178	50	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	75.9974	74	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_002549795.1	s__Halomonas beimenensis	75.9764	61	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889815.1	s__UBA5078 sp903889815	75.9627	75	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	75.9474	55	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641755.2	s__Microbulbifer flavimaris	75.9338	54	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900187975.1	s__Pseudomonas delhiensis	75.9189	88	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCA_903862645.1	s__UBA5078 sp903862645	75.8702	65	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012795.1	s__Zobellella_D taiwanensis	75.7821	58	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091635.1	s__Pseudomonas_M indica	75.4086	61	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-14 11:16:14,325] [INFO] GTDB search result was written to OceanDNA-b40232/result_gtdb.tsv
[2023-03-14 11:16:14,325] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:16:14,328] [INFO] DFAST_QC result json was written to OceanDNA-b40232/dqc_result.json
[2023-03-14 11:16:14,328] [INFO] DFAST_QC completed!
[2023-03-14 11:16:14,328] [INFO] Total running time: 0h2m2s