[2023-03-17 05:53:20,813] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:53:20,813] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:53:20,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a84403f-c717-4fe5-a10a-98dcd2112fc5/dqc_reference
[2023-03-17 05:53:21,979] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:53:21,979] [INFO] Task started: Prodigal
[2023-03-17 05:53:21,979] [INFO] Running command: cat /var/lib/cwl/stg18d3a758-039f-4e06-b696-f604c36bfeda/OceanDNA-b35303.fa | prodigal -d OceanDNA-b35303/cds.fna -a OceanDNA-b35303/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:53:40,601] [INFO] Task succeeded: Prodigal
[2023-03-17 05:53:40,601] [INFO] Task started: HMMsearch
[2023-03-17 05:53:40,601] [INFO] Running command: hmmsearch --tblout OceanDNA-b35303/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a84403f-c717-4fe5-a10a-98dcd2112fc5/dqc_reference/reference_markers.hmm OceanDNA-b35303/protein.faa > /dev/null
[2023-03-17 05:53:40,822] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:53:40,823] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg18d3a758-039f-4e06-b696-f604c36bfeda/OceanDNA-b35303.fa]
[2023-03-17 05:53:40,848] [INFO] Query marker FASTA was written to OceanDNA-b35303/markers.fasta
[2023-03-17 05:53:40,849] [INFO] Task started: Blastn
[2023-03-17 05:53:40,849] [INFO] Running command: blastn -query OceanDNA-b35303/markers.fasta -db /var/lib/cwl/stg4a84403f-c717-4fe5-a10a-98dcd2112fc5/dqc_reference/reference_markers.fasta -out OceanDNA-b35303/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:53:41,563] [INFO] Task succeeded: Blastn
[2023-03-17 05:53:41,564] [INFO] Selected 13 target genomes.
[2023-03-17 05:53:41,564] [INFO] Target genome list was writen to OceanDNA-b35303/target_genomes.txt
[2023-03-17 05:53:41,607] [INFO] Task started: fastANI
[2023-03-17 05:53:41,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg18d3a758-039f-4e06-b696-f604c36bfeda/OceanDNA-b35303.fa --refList OceanDNA-b35303/target_genomes.txt --output OceanDNA-b35303/fastani_result.tsv --threads 1
[2023-03-17 05:53:54,595] [INFO] Task succeeded: fastANI
[2023-03-17 05:53:54,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a84403f-c717-4fe5-a10a-98dcd2112fc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:53:54,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a84403f-c717-4fe5-a10a-98dcd2112fc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:53:54,604] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 05:53:54,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:53:54,604] [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
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	97.8272	1003	1053	95	conclusive
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	91.1258	950	1053	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	89.7242	916	1053	95	below_threshold
Vibrio harveyi	strain=ATCC 14126	GCA_001263135.1	669	669	type	True	89.7073	899	1053	95	below_threshold
Vibrio harveyi	strain=NCTC12970	GCA_900460165.1	669	669	type	True	89.6948	926	1053	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	89.4414	865	1053	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	88.568	936	1053	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	88.5065	936	1053	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	82.6126	620	1053	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.9889	314	1053	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.9297	309	1053	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.5383	400	1053	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.4961	400	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:53:54,611] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35303/tc_result.tsv
[2023-03-17 05:53:54,621] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:53:54,621] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:53:54,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a84403f-c717-4fe5-a10a-98dcd2112fc5/dqc_reference/checkm_data
[2023-03-17 05:53:54,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:53:54,634] [INFO] Task started: CheckM
[2023-03-17 05:53:54,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35303/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35303/checkm_input OceanDNA-b35303/checkm_result
[2023-03-17 05:54:43,822] [INFO] Task succeeded: CheckM
[2023-03-17 05:54:43,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:54:43,949] [INFO] ===== Completeness check finished =====
[2023-03-17 05:54:43,949] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:54:43,949] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35303/markers.fasta)
[2023-03-17 05:54:43,950] [INFO] Task started: Blastn
[2023-03-17 05:54:43,950] [INFO] Running command: blastn -query OceanDNA-b35303/markers.fasta -db /var/lib/cwl/stg4a84403f-c717-4fe5-a10a-98dcd2112fc5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35303/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:54:44,960] [INFO] Task succeeded: Blastn
[2023-03-17 05:54:44,961] [INFO] Selected 9 target genomes.
[2023-03-17 05:54:44,961] [INFO] Target genome list was writen to OceanDNA-b35303/target_genomes_gtdb.txt
[2023-03-17 05:54:44,968] [INFO] Task started: fastANI
[2023-03-17 05:54:44,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg18d3a758-039f-4e06-b696-f604c36bfeda/OceanDNA-b35303.fa --refList OceanDNA-b35303/target_genomes_gtdb.txt --output OceanDNA-b35303/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:54:55,012] [INFO] Task succeeded: fastANI
[2023-03-17 05:54:55,019] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:54:55,019] [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_002163755.1	s__Vibrio campbellii	97.9726	1028	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	conclusive
GCF_000817815.1	s__Vibrio owensii	91.1258	950	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_001591145.1	s__Vibrio harveyi	89.7242	916	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_002741985.1	s__Vibrio rotiferianus	89.4414	865	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000400365.1	s__Vibrio jasicida	89.1883	942	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002906655.1	s__Vibrio hyugaensis	88.5123	935	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_000171815.1	s__Vibrio sp000171815	86.2496	756	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000354175.2	s__Vibrio alginolyticus	84.5518	746	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCA_001048675.1	s__Vibrio diabolicus	83.8615	763	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
--------------------------------------------------------------------------------
[2023-03-17 05:54:55,022] [INFO] GTDB search result was written to OceanDNA-b35303/result_gtdb.tsv
[2023-03-17 05:54:55,024] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:54:55,028] [INFO] DFAST_QC result json was written to OceanDNA-b35303/dqc_result.json
[2023-03-17 05:54:55,028] [INFO] DFAST_QC completed!
[2023-03-17 05:54:55,028] [INFO] Total running time: 0h1m34s