[2023-03-18 03:45:10,278] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,279] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,279] [INFO] DQC Reference Directory: /var/lib/cwl/stg33c221c0-8729-4e52-b02b-8128b56b3e9a/dqc_reference
[2023-03-18 03:45:12,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,142] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,142] [INFO] Running command: cat /var/lib/cwl/stg771b3dc0-67d8-445d-bcbc-60438974e5b1/OceanDNA-b37658.fa | prodigal -d OceanDNA-b37658/cds.fna -a OceanDNA-b37658/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:32,376] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:32,376] [INFO] Task started: HMMsearch
[2023-03-18 03:45:32,376] [INFO] Running command: hmmsearch --tblout OceanDNA-b37658/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33c221c0-8729-4e52-b02b-8128b56b3e9a/dqc_reference/reference_markers.hmm OceanDNA-b37658/protein.faa > /dev/null
[2023-03-18 03:45:32,652] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:32,653] [INFO] Found 6/6 markers.
[2023-03-18 03:45:32,677] [INFO] Query marker FASTA was written to OceanDNA-b37658/markers.fasta
[2023-03-18 03:45:32,677] [INFO] Task started: Blastn
[2023-03-18 03:45:32,677] [INFO] Running command: blastn -query OceanDNA-b37658/markers.fasta -db /var/lib/cwl/stg33c221c0-8729-4e52-b02b-8128b56b3e9a/dqc_reference/reference_markers.fasta -out OceanDNA-b37658/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:33,321] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:33,321] [INFO] Selected 25 target genomes.
[2023-03-18 03:45:33,322] [INFO] Target genome list was writen to OceanDNA-b37658/target_genomes.txt
[2023-03-18 03:45:33,329] [INFO] Task started: fastANI
[2023-03-18 03:45:33,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg771b3dc0-67d8-445d-bcbc-60438974e5b1/OceanDNA-b37658.fa --refList OceanDNA-b37658/target_genomes.txt --output OceanDNA-b37658/fastani_result.tsv --threads 1
[2023-03-18 03:45:49,413] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:49,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33c221c0-8729-4e52-b02b-8128b56b3e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:49,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33c221c0-8729-4e52-b02b-8128b56b3e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:49,421] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:49,421] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:49,421] [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
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.5598	260	1107	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.4713	249	1107	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	77.3274	150	1107	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.0735	92	1107	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.9474	156	1107	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.9342	157	1107	95	below_threshold
Pseudohalioglobus lutimaris	strain=HF004	GCA_002866825.1	1737061	1737061	type	True	76.932	163	1107	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.8947	159	1107	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.8212	94	1107	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.7472	99	1107	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.501	70	1107	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.3937	73	1107	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:49,421] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37658/tc_result.tsv
[2023-03-18 03:45:49,422] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:49,422] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:49,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33c221c0-8729-4e52-b02b-8128b56b3e9a/dqc_reference/checkm_data
[2023-03-18 03:45:49,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:49,501] [INFO] Task started: CheckM
[2023-03-18 03:45:49,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37658/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37658/checkm_input OceanDNA-b37658/checkm_result
[2023-03-18 03:46:40,771] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:40,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:40,774] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:40,774] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:40,774] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37658/markers.fasta)
[2023-03-18 03:46:40,775] [INFO] Task started: Blastn
[2023-03-18 03:46:40,775] [INFO] Running command: blastn -query OceanDNA-b37658/markers.fasta -db /var/lib/cwl/stg33c221c0-8729-4e52-b02b-8128b56b3e9a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37658/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:41,851] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:41,852] [INFO] Selected 20 target genomes.
[2023-03-18 03:46:41,852] [INFO] Target genome list was writen to OceanDNA-b37658/target_genomes_gtdb.txt
[2023-03-18 03:46:41,969] [INFO] Task started: fastANI
[2023-03-18 03:46:41,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg771b3dc0-67d8-445d-bcbc-60438974e5b1/OceanDNA-b37658.fa --refList OceanDNA-b37658/target_genomes_gtdb.txt --output OceanDNA-b37658/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:55,561] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:55,569] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:46:55,569] [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_000156295.1	s__Halioglobus sp000156295	98.6358	1069	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.94	98.78	0.94	0.91	6	conclusive
GCA_004354085.1	s__Halioglobus sp004354085	77.5598	260	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	77.4713	249	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009388985.1	s__Halioglobus maricola	77.3274	150	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	77.3059	178	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002866825.1	s__Halioglobus lutimaris	76.932	163	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.98	98.98	0.91	0.91	2	-
GCF_001983995.1	s__Halioglobus japonicus	76.9093	158	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_008064635.1	s__Parahaliea aestuarii	76.8212	94	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.7691	98	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868715.1	s__Kineobactrum sediminis	76.501	70	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.3958	90	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002416125.1	s__Haliea sp002416125	76.2839	65	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCA_002692965.1	s__NZNC01 sp002692965	76.2834	60	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_902705825.1	s__Halioglobus japonicus_A	76.1906	72	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:55,570] [INFO] GTDB search result was written to OceanDNA-b37658/result_gtdb.tsv
[2023-03-18 03:46:55,570] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:55,571] [INFO] DFAST_QC result json was written to OceanDNA-b37658/dqc_result.json
[2023-03-18 03:46:55,571] [INFO] DFAST_QC completed!
[2023-03-18 03:46:55,571] [INFO] Total running time: 0h1m45s