[2023-03-17 06:30:49,799] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,799] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,800] [INFO] DQC Reference Directory: /var/lib/cwl/stged2470cb-2c26-4cf8-8757-c549fac25072/dqc_reference
[2023-03-17 06:30:51,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:51,354] [INFO] Task started: Prodigal
[2023-03-17 06:30:51,354] [INFO] Running command: cat /var/lib/cwl/stgfd93a126-42ba-436b-bd4f-abadcb59939f/OceanDNA-b36676.fa | prodigal -d OceanDNA-b36676/cds.fna -a OceanDNA-b36676/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:15,433] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:15,433] [INFO] Task started: HMMsearch
[2023-03-17 06:31:15,433] [INFO] Running command: hmmsearch --tblout OceanDNA-b36676/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged2470cb-2c26-4cf8-8757-c549fac25072/dqc_reference/reference_markers.hmm OceanDNA-b36676/protein.faa > /dev/null
[2023-03-17 06:31:15,650] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:15,650] [INFO] Found 6/6 markers.
[2023-03-17 06:31:15,674] [INFO] Query marker FASTA was written to OceanDNA-b36676/markers.fasta
[2023-03-17 06:31:15,674] [INFO] Task started: Blastn
[2023-03-17 06:31:15,674] [INFO] Running command: blastn -query OceanDNA-b36676/markers.fasta -db /var/lib/cwl/stged2470cb-2c26-4cf8-8757-c549fac25072/dqc_reference/reference_markers.fasta -out OceanDNA-b36676/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:16,300] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:16,301] [INFO] Selected 27 target genomes.
[2023-03-17 06:31:16,301] [INFO] Target genome list was writen to OceanDNA-b36676/target_genomes.txt
[2023-03-17 06:31:16,314] [INFO] Task started: fastANI
[2023-03-17 06:31:16,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd93a126-42ba-436b-bd4f-abadcb59939f/OceanDNA-b36676.fa --refList OceanDNA-b36676/target_genomes.txt --output OceanDNA-b36676/fastani_result.tsv --threads 1
[2023-03-17 06:31:34,609] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:34,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged2470cb-2c26-4cf8-8757-c549fac25072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:34,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged2470cb-2c26-4cf8-8757-c549fac25072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:34,618] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:34,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:34,618] [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
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	79.8485	635	1352	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	77.7657	310	1352	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	76.4472	100	1352	95	below_threshold
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	76.3503	92	1352	95	below_threshold
Aestuariicella hydrocarbonica	strain=JCM 30134	GCA_011602365.1	1470433	1470433	type	True	76.2857	69	1352	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	76.2813	112	1352	95	below_threshold
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	76.1438	57	1352	95	below_threshold
Pseudomaricurvus alkylphenolicus	strain=KCTC 32386	GCA_011683955.1	1306991	1306991	type	True	76.1376	63	1352	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.0099	58	1352	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	75.8543	60	1352	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	75.834	59	1352	95	below_threshold
Exilibacterium tricleocarpae	strain=R142	GCA_007004655.1	2591008	2591008	type	True	75.6741	53	1352	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:34,618] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36676/tc_result.tsv
[2023-03-17 06:31:34,618] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:34,618] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:34,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged2470cb-2c26-4cf8-8757-c549fac25072/dqc_reference/checkm_data
[2023-03-17 06:31:34,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:34,659] [INFO] Task started: CheckM
[2023-03-17 06:31:34,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36676/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36676/checkm_input OceanDNA-b36676/checkm_result
[2023-03-17 06:32:33,321] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:33,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:33,324] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:33,324] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:33,324] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36676/markers.fasta)
[2023-03-17 06:32:33,325] [INFO] Task started: Blastn
[2023-03-17 06:32:33,325] [INFO] Running command: blastn -query OceanDNA-b36676/markers.fasta -db /var/lib/cwl/stged2470cb-2c26-4cf8-8757-c549fac25072/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36676/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:34,357] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:34,357] [INFO] Selected 24 target genomes.
[2023-03-17 06:32:34,357] [INFO] Target genome list was writen to OceanDNA-b36676/target_genomes_gtdb.txt
[2023-03-17 06:32:34,696] [INFO] Task started: fastANI
[2023-03-17 06:32:34,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd93a126-42ba-436b-bd4f-abadcb59939f/OceanDNA-b36676.fa --refList OceanDNA-b36676/target_genomes_gtdb.txt --output OceanDNA-b36676/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:50,882] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:50,890] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:50,891] [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_000832015.1	s__Gilvimarinus agarilyticus	82.4094	785	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187555.1	s__Gilvimarinus polysaccharolyticus	79.855	635	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377745.1	s__Gilvimarinus chinensis	77.7768	312	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	76.4472	100	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423345.1	s__Marinimicrobium agarilyticum	76.3503	92	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	76.3175	70	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259155.1	s__Marinimicrobium_A alkaliphilum	76.2813	112	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953825.1	s__Cellvibrio sp000953825	76.0129	97	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806955.1	s__Cellvibrio sp000263355	75.9885	89	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCF_004363885.1	s__Cellvibrio sp004363885	75.9745	75	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	75.7772	69	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483145.1	s__Cellvibrio sp002483145	75.7277	72	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004655.1	s__Exilibacterium tricleocarpae	75.6954	52	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Exilibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007827375.1	s__Teredinibacter sp007827375	75.6417	50	1352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:50,891] [INFO] GTDB search result was written to OceanDNA-b36676/result_gtdb.tsv
[2023-03-17 06:32:50,891] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:50,892] [INFO] DFAST_QC result json was written to OceanDNA-b36676/dqc_result.json
[2023-03-17 06:32:50,893] [INFO] DFAST_QC completed!
[2023-03-17 06:32:50,893] [INFO] Total running time: 0h2m1s