[2023-03-15 06:03:50,875] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:03:50,876] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:03:50,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg3147ed36-3ac9-45b4-99e0-4787fff57b76/dqc_reference
[2023-03-15 06:03:52,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:03:52,058] [INFO] Task started: Prodigal
[2023-03-15 06:03:52,058] [INFO] Running command: cat /var/lib/cwl/stga1992d65-0528-44db-ad24-fea326c38d86/OceanDNA-b37543.fa | prodigal -d OceanDNA-b37543/cds.fna -a OceanDNA-b37543/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:04:14,589] [INFO] Task succeeded: Prodigal
[2023-03-15 06:04:14,589] [INFO] Task started: HMMsearch
[2023-03-15 06:04:14,589] [INFO] Running command: hmmsearch --tblout OceanDNA-b37543/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3147ed36-3ac9-45b4-99e0-4787fff57b76/dqc_reference/reference_markers.hmm OceanDNA-b37543/protein.faa > /dev/null
[2023-03-15 06:04:14,780] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:04:14,781] [INFO] Found 6/6 markers.
[2023-03-15 06:04:14,803] [INFO] Query marker FASTA was written to OceanDNA-b37543/markers.fasta
[2023-03-15 06:04:14,804] [INFO] Task started: Blastn
[2023-03-15 06:04:14,804] [INFO] Running command: blastn -query OceanDNA-b37543/markers.fasta -db /var/lib/cwl/stg3147ed36-3ac9-45b4-99e0-4787fff57b76/dqc_reference/reference_markers.fasta -out OceanDNA-b37543/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:04:15,525] [INFO] Task succeeded: Blastn
[2023-03-15 06:04:15,526] [INFO] Selected 18 target genomes.
[2023-03-15 06:04:15,526] [INFO] Target genome list was writen to OceanDNA-b37543/target_genomes.txt
[2023-03-15 06:04:15,537] [INFO] Task started: fastANI
[2023-03-15 06:04:15,537] [INFO] Running command: fastANI --query /var/lib/cwl/stga1992d65-0528-44db-ad24-fea326c38d86/OceanDNA-b37543.fa --refList OceanDNA-b37543/target_genomes.txt --output OceanDNA-b37543/fastani_result.tsv --threads 1
[2023-03-15 06:04:28,599] [INFO] Task succeeded: fastANI
[2023-03-15 06:04:28,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3147ed36-3ac9-45b4-99e0-4787fff57b76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:04:28,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3147ed36-3ac9-45b4-99e0-4787fff57b76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:04:28,611] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:04:28,611] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:04:28,611] [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
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	81.5737	820	1177	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	81.5726	834	1177	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.5948	370	1177	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	78.2188	326	1177	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.9321	346	1177	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.8137	315	1177	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.7337	290	1177	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.9893	156	1177	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	76.8385	183	1177	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.4578	121	1177	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.4505	92	1177	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.2963	88	1177	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.2757	89	1177	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.216	89	1177	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	76.1512	122	1177	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.1468	122	1177	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.0633	122	1177	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.0255	71	1177	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:04:28,611] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37543/tc_result.tsv
[2023-03-15 06:04:28,611] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:04:28,611] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:04:28,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3147ed36-3ac9-45b4-99e0-4787fff57b76/dqc_reference/checkm_data
[2023-03-15 06:04:28,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:04:28,617] [INFO] Task started: CheckM
[2023-03-15 06:04:28,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37543/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37543/checkm_input OceanDNA-b37543/checkm_result
[2023-03-15 06:05:24,849] [INFO] Task succeeded: CheckM
[2023-03-15 06:05:24,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:05:24,921] [INFO] ===== Completeness check finished =====
[2023-03-15 06:05:24,921] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:05:24,922] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37543/markers.fasta)
[2023-03-15 06:05:24,923] [INFO] Task started: Blastn
[2023-03-15 06:05:24,923] [INFO] Running command: blastn -query OceanDNA-b37543/markers.fasta -db /var/lib/cwl/stg3147ed36-3ac9-45b4-99e0-4787fff57b76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37543/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:05:26,190] [INFO] Task succeeded: Blastn
[2023-03-15 06:05:26,196] [INFO] Selected 10 target genomes.
[2023-03-15 06:05:26,196] [INFO] Target genome list was writen to OceanDNA-b37543/target_genomes_gtdb.txt
[2023-03-15 06:05:26,207] [INFO] Task started: fastANI
[2023-03-15 06:05:26,207] [INFO] Running command: fastANI --query /var/lib/cwl/stga1992d65-0528-44db-ad24-fea326c38d86/OceanDNA-b37543.fa --refList OceanDNA-b37543/target_genomes_gtdb.txt --output OceanDNA-b37543/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:05:34,284] [INFO] Task succeeded: fastANI
[2023-03-15 06:05:34,291] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:05:34,291] [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_002416125.1	s__Haliea sp002416125	94.6609	1053	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCA_002414665.1	s__Haliea sp002414665	91.784	1033	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCF_000423125.1	s__Haliea salexigens	81.5726	834	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_003719295.1	s__Haliea alexandrii	81.5651	821	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	78.4143	397	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_010669285.1	s__Kineobactrum salinum	78.2079	327	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.9198	348	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	77.7933	317	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	77.6198	309	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_008370495.1	s__Halioglobus sp008370495	77.0058	196	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:05:34,294] [INFO] GTDB search result was written to OceanDNA-b37543/result_gtdb.tsv
[2023-03-15 06:05:34,300] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:05:34,306] [INFO] DFAST_QC result json was written to OceanDNA-b37543/dqc_result.json
[2023-03-15 06:05:34,306] [INFO] DFAST_QC completed!
[2023-03-15 06:05:34,306] [INFO] Total running time: 0h1m43s