[2023-03-17 05:31:30,561] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:31:30,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:31:30,561] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4ed3176-08b7-4f00-9f90-ea2d4c3d4f45/dqc_reference
[2023-03-17 05:31:33,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:31:33,266] [INFO] Task started: Prodigal
[2023-03-17 05:31:33,266] [INFO] Running command: cat /var/lib/cwl/stg65c19697-703b-4da2-a521-b66d4f7a0d63/OceanDNA-b35313.fa | prodigal -d OceanDNA-b35313/cds.fna -a OceanDNA-b35313/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:31:42,803] [INFO] Task succeeded: Prodigal
[2023-03-17 05:31:42,804] [INFO] Task started: HMMsearch
[2023-03-17 05:31:42,804] [INFO] Running command: hmmsearch --tblout OceanDNA-b35313/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4ed3176-08b7-4f00-9f90-ea2d4c3d4f45/dqc_reference/reference_markers.hmm OceanDNA-b35313/protein.faa > /dev/null
[2023-03-17 05:31:43,037] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:31:43,037] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg65c19697-703b-4da2-a521-b66d4f7a0d63/OceanDNA-b35313.fa]
[2023-03-17 05:31:43,061] [INFO] Query marker FASTA was written to OceanDNA-b35313/markers.fasta
[2023-03-17 05:31:43,063] [INFO] Task started: Blastn
[2023-03-17 05:31:43,063] [INFO] Running command: blastn -query OceanDNA-b35313/markers.fasta -db /var/lib/cwl/stgc4ed3176-08b7-4f00-9f90-ea2d4c3d4f45/dqc_reference/reference_markers.fasta -out OceanDNA-b35313/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:31:46,380] [INFO] Task succeeded: Blastn
[2023-03-17 05:31:46,381] [INFO] Selected 12 target genomes.
[2023-03-17 05:31:46,382] [INFO] Target genome list was writen to OceanDNA-b35313/target_genomes.txt
[2023-03-17 05:31:46,390] [INFO] Task started: fastANI
[2023-03-17 05:31:46,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c19697-703b-4da2-a521-b66d4f7a0d63/OceanDNA-b35313.fa --refList OceanDNA-b35313/target_genomes.txt --output OceanDNA-b35313/fastani_result.tsv --threads 1
[2023-03-17 05:31:55,116] [INFO] Task succeeded: fastANI
[2023-03-17 05:31:55,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4ed3176-08b7-4f00-9f90-ea2d4c3d4f45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:31:55,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4ed3176-08b7-4f00-9f90-ea2d4c3d4f45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:31:55,176] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:31:55,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:31:55,177] [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 pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	92.7836	280	307	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	91.0203	295	307	95	below_threshold
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	84.3439	230	307	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	84.3409	235	307	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	84.2816	232	307	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	84.0808	235	307	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	83.9066	226	307	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	83.6076	234	307	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	83.5956	237	307	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	83.3705	216	307	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	83.3619	217	307	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	83.343	218	307	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:31:55,177] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35313/tc_result.tsv
[2023-03-17 05:31:55,177] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:31:55,177] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:31:55,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4ed3176-08b7-4f00-9f90-ea2d4c3d4f45/dqc_reference/checkm_data
[2023-03-17 05:31:55,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:31:55,183] [INFO] Task started: CheckM
[2023-03-17 05:31:55,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35313/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35313/checkm_input OceanDNA-b35313/checkm_result
[2023-03-17 05:32:29,805] [INFO] Task succeeded: CheckM
[2023-03-17 05:32:29,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:32:29,808] [INFO] ===== Completeness check finished =====
[2023-03-17 05:32:29,808] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:32:29,808] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35313/markers.fasta)
[2023-03-17 05:32:29,809] [INFO] Task started: Blastn
[2023-03-17 05:32:29,809] [INFO] Running command: blastn -query OceanDNA-b35313/markers.fasta -db /var/lib/cwl/stgc4ed3176-08b7-4f00-9f90-ea2d4c3d4f45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35313/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:32:31,042] [INFO] Task succeeded: Blastn
[2023-03-17 05:32:31,043] [INFO] Selected 13 target genomes.
[2023-03-17 05:32:31,043] [INFO] Target genome list was writen to OceanDNA-b35313/target_genomes_gtdb.txt
[2023-03-17 05:32:31,073] [INFO] Task started: fastANI
[2023-03-17 05:32:31,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c19697-703b-4da2-a521-b66d4f7a0d63/OceanDNA-b35313.fa --refList OceanDNA-b35313/target_genomes_gtdb.txt --output OceanDNA-b35313/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:32:40,826] [INFO] Task succeeded: fastANI
[2023-03-17 05:32:40,835] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:32:40,835] [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_000695685.1	s__Vibrio fortis	96.9972	300	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	conclusive
GCF_002954585.1	s__Vibrio chagasii_A	84.5566	224	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_001635455.1	s__Vibrio sp001635455	84.3799	212	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281815.1	s__Vibrio chagasii	84.2816	232	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCA_000169995.1	s__Vibrio sp000169995	84.2589	220	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875945.1	s__Vibrio lentus_A	83.8238	226	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	83.7384	227	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_001048535.1	s__Vibrio crassostreae	83.6661	233	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_002156475.1	s__Vibrio gigantis	83.5956	237	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_006333845.1	s__Vibrio tasmaniensis	83.3619	217	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_004764665.1	s__Vibrio echinoideorum	83.2017	224	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_008801285.1	s__Vibrio kanaloae	82.7124	226	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_003415655.1	s__Vibrio maerlii	80.0071	138	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:32:40,835] [INFO] GTDB search result was written to OceanDNA-b35313/result_gtdb.tsv
[2023-03-17 05:32:40,835] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:32:40,837] [INFO] DFAST_QC result json was written to OceanDNA-b35313/dqc_result.json
[2023-03-17 05:32:40,837] [INFO] DFAST_QC completed!
[2023-03-17 05:32:40,837] [INFO] Total running time: 0h1m10s