[2023-03-19 00:15:41,729] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,729] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf0d5da2-fc22-42b6-983d-72e54453c574/dqc_reference
[2023-03-19 00:15:43,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,441] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,441] [INFO] Running command: cat /var/lib/cwl/stg0aa03ebb-46b7-4887-8f7d-44559e54e9b5/OceanDNA-b37573.fa | prodigal -d OceanDNA-b37573/cds.fna -a OceanDNA-b37573/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:10,362] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:10,362] [INFO] Task started: HMMsearch
[2023-03-19 00:16:10,362] [INFO] Running command: hmmsearch --tblout OceanDNA-b37573/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf0d5da2-fc22-42b6-983d-72e54453c574/dqc_reference/reference_markers.hmm OceanDNA-b37573/protein.faa > /dev/null
[2023-03-19 00:16:10,595] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:10,596] [INFO] Found 6/6 markers.
[2023-03-19 00:16:10,621] [INFO] Query marker FASTA was written to OceanDNA-b37573/markers.fasta
[2023-03-19 00:16:10,622] [INFO] Task started: Blastn
[2023-03-19 00:16:10,622] [INFO] Running command: blastn -query OceanDNA-b37573/markers.fasta -db /var/lib/cwl/stgdf0d5da2-fc22-42b6-983d-72e54453c574/dqc_reference/reference_markers.fasta -out OceanDNA-b37573/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:11,362] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:11,363] [INFO] Selected 15 target genomes.
[2023-03-19 00:16:11,363] [INFO] Target genome list was writen to OceanDNA-b37573/target_genomes.txt
[2023-03-19 00:16:11,373] [INFO] Task started: fastANI
[2023-03-19 00:16:11,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa03ebb-46b7-4887-8f7d-44559e54e9b5/OceanDNA-b37573.fa --refList OceanDNA-b37573/target_genomes.txt --output OceanDNA-b37573/fastani_result.tsv --threads 1
[2023-03-19 00:16:24,426] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:24,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf0d5da2-fc22-42b6-983d-72e54453c574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:24,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf0d5da2-fc22-42b6-983d-72e54453c574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:24,440] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 00:16:24,440] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 00:16:24,440] [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 salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	96.7852	1163	1364	95	conclusive
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	93.1195	1109	1364	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	78.1961	338	1364	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.1377	423	1364	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.9699	306	1364	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.8373	356	1364	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.7593	325	1364	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	76.8288	197	1364	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.5601	134	1364	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4846	121	1364	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.4552	95	1364	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.3898	98	1364	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.2853	118	1364	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	75.8149	75	1364	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	75.6009	63	1364	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:24,441] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37573/tc_result.tsv
[2023-03-19 00:16:24,441] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:24,441] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:24,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf0d5da2-fc22-42b6-983d-72e54453c574/dqc_reference/checkm_data
[2023-03-19 00:16:24,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:24,449] [INFO] Task started: CheckM
[2023-03-19 00:16:24,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37573/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37573/checkm_input OceanDNA-b37573/checkm_result
[2023-03-19 00:17:28,188] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:28,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:28,191] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:28,191] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:28,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37573/markers.fasta)
[2023-03-19 00:17:28,193] [INFO] Task started: Blastn
[2023-03-19 00:17:28,193] [INFO] Running command: blastn -query OceanDNA-b37573/markers.fasta -db /var/lib/cwl/stgdf0d5da2-fc22-42b6-983d-72e54453c574/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37573/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:29,581] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:29,596] [INFO] Selected 8 target genomes.
[2023-03-19 00:17:29,596] [INFO] Target genome list was writen to OceanDNA-b37573/target_genomes_gtdb.txt
[2023-03-19 00:17:29,625] [INFO] Task started: fastANI
[2023-03-19 00:17:29,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa03ebb-46b7-4887-8f7d-44559e54e9b5/OceanDNA-b37573.fa --refList OceanDNA-b37573/target_genomes_gtdb.txt --output OceanDNA-b37573/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:36,524] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:36,530] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:36,530] [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_000423125.1	s__Haliea salexigens	96.7879	1162	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	conclusive
GCF_003719295.1	s__Haliea alexandrii	93.1195	1109	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414665.1	s__Haliea sp002414665	82.1764	819	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCA_002416125.1	s__Haliea sp002416125	81.566	819	1364	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	78.8852	421	1364	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	78.2074	337	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868715.1	s__Kineobactrum sediminis	77.9745	307	1364	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	77.8343	357	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:36,531] [INFO] GTDB search result was written to OceanDNA-b37573/result_gtdb.tsv
[2023-03-19 00:17:36,531] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:36,533] [INFO] DFAST_QC result json was written to OceanDNA-b37573/dqc_result.json
[2023-03-19 00:17:36,533] [INFO] DFAST_QC completed!
[2023-03-19 00:17:36,533] [INFO] Total running time: 0h1m55s