[2023-03-17 01:23:45,160] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,161] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,161] [INFO] DQC Reference Directory: /var/lib/cwl/stg71491ce6-5b25-48d2-9f66-e5edf7e100b6/dqc_reference
[2023-03-17 01:23:46,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,318] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,318] [INFO] Running command: cat /var/lib/cwl/stg640dae92-1797-496e-b2d8-29d1b39b0501/OceanDNA-b38182.fa | prodigal -d OceanDNA-b38182/cds.fna -a OceanDNA-b38182/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:24:08,068] [INFO] Task succeeded: Prodigal
[2023-03-17 01:24:08,069] [INFO] Task started: HMMsearch
[2023-03-17 01:24:08,069] [INFO] Running command: hmmsearch --tblout OceanDNA-b38182/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71491ce6-5b25-48d2-9f66-e5edf7e100b6/dqc_reference/reference_markers.hmm OceanDNA-b38182/protein.faa > /dev/null
[2023-03-17 01:24:08,275] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:24:08,276] [INFO] Found 6/6 markers.
[2023-03-17 01:24:08,295] [INFO] Query marker FASTA was written to OceanDNA-b38182/markers.fasta
[2023-03-17 01:24:08,296] [INFO] Task started: Blastn
[2023-03-17 01:24:08,296] [INFO] Running command: blastn -query OceanDNA-b38182/markers.fasta -db /var/lib/cwl/stg71491ce6-5b25-48d2-9f66-e5edf7e100b6/dqc_reference/reference_markers.fasta -out OceanDNA-b38182/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:09,149] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:09,150] [INFO] Selected 12 target genomes.
[2023-03-17 01:24:09,150] [INFO] Target genome list was writen to OceanDNA-b38182/target_genomes.txt
[2023-03-17 01:24:09,157] [INFO] Task started: fastANI
[2023-03-17 01:24:09,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg640dae92-1797-496e-b2d8-29d1b39b0501/OceanDNA-b38182.fa --refList OceanDNA-b38182/target_genomes.txt --output OceanDNA-b38182/fastani_result.tsv --threads 1
[2023-03-17 01:24:18,760] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:18,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71491ce6-5b25-48d2-9f66-e5edf7e100b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:18,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71491ce6-5b25-48d2-9f66-e5edf7e100b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:18,768] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 01:24:18,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 01:24:18,769] [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
Chromohalobacter salexigens	strain=DSM 3043	GCA_000055785.1	158080	158080	type	True	98.5161	1043	1129	95	conclusive
Chromohalobacter marismortui	strain=DSM 6770	GCA_004364315.1	42055	42055	type	True	86.7935	902	1129	95	below_threshold
Chromohalobacter moromii	strain=TMW 2.2308	GCA_023091865.1	2860329	2860329	type	True	86.0244	895	1129	95	below_threshold
Chromohalobacter beijerinckii	strain=DSM 7218	GCA_023061185.1	86179	86179	type	True	85.8397	852	1129	95	below_threshold
Chromohalobacter canadensis	strain=DSM 6769	GCA_023061155.1	141389	141389	suspected-type	True	85.5785	883	1129	95	below_threshold
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	85.4396	861	1129	95	below_threshold
Chromohalobacter sarecensis	strain=DSM 15547	GCA_023061135.1	245294	245294	type	True	83.848	856	1129	95	below_threshold
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	83.7883	860	1129	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	79.7909	448	1129	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	79.7616	489	1129	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	79.7003	472	1129	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	79.6397	458	1129	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:24:18,769] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38182/tc_result.tsv
[2023-03-17 01:24:18,769] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:18,769] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:18,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71491ce6-5b25-48d2-9f66-e5edf7e100b6/dqc_reference/checkm_data
[2023-03-17 01:24:18,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:18,774] [INFO] Task started: CheckM
[2023-03-17 01:24:18,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38182/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38182/checkm_input OceanDNA-b38182/checkm_result
[2023-03-17 01:25:15,253] [INFO] Task succeeded: CheckM
[2023-03-17 01:25:15,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:25:15,257] [INFO] ===== Completeness check finished =====
[2023-03-17 01:25:15,257] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:25:15,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38182/markers.fasta)
[2023-03-17 01:25:15,257] [INFO] Task started: Blastn
[2023-03-17 01:25:15,257] [INFO] Running command: blastn -query OceanDNA-b38182/markers.fasta -db /var/lib/cwl/stg71491ce6-5b25-48d2-9f66-e5edf7e100b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38182/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:25:16,836] [INFO] Task succeeded: Blastn
[2023-03-17 01:25:16,837] [INFO] Selected 10 target genomes.
[2023-03-17 01:25:16,837] [INFO] Target genome list was writen to OceanDNA-b38182/target_genomes_gtdb.txt
[2023-03-17 01:25:16,955] [INFO] Task started: fastANI
[2023-03-17 01:25:16,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg640dae92-1797-496e-b2d8-29d1b39b0501/OceanDNA-b38182.fa --refList OceanDNA-b38182/target_genomes_gtdb.txt --output OceanDNA-b38182/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:25:24,825] [INFO] Task succeeded: fastANI
[2023-03-17 01:25:24,831] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:25:24,831] [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_000761475.1	s__Chromohalobacter israelensis	98.2697	987	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	98.07	97.76	0.86	0.85	6	conclusive
GCF_004364315.1	s__Chromohalobacter marismortui	86.7934	902	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393405.1	s__Chromohalobacter salexigens_A	86.3316	854	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900221025.1	s__Chromohalobacter canadensis	85.4905	889	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821045.2	s__Chromohalobacter japonicus	85.4688	857	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	95.33	95.33	0.87	0.87	2	-
GCF_004117855.1	s__Halomonas_C coralii	80.4813	624	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989465.1	s__Halomonas halophila	80.1793	523	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_001886615.1	s__Halomonas aestuarii	79.7908	448	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	79.7063	472	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_003182195.1	s__Halomonas sp003182195	79.3952	415	1129	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-17 01:25:24,831] [INFO] GTDB search result was written to OceanDNA-b38182/result_gtdb.tsv
[2023-03-17 01:25:24,831] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:25:24,833] [INFO] DFAST_QC result json was written to OceanDNA-b38182/dqc_result.json
[2023-03-17 01:25:24,833] [INFO] DFAST_QC completed!
[2023-03-17 01:25:24,833] [INFO] Total running time: 0h1m40s