[2023-03-18 09:58:36,588] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:58:36,588] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:58:36,588] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2754e53-5fbd-4758-9696-aed79ec0ff06/dqc_reference
[2023-03-18 09:58:38,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:58:38,403] [INFO] Task started: Prodigal
[2023-03-18 09:58:38,403] [INFO] Running command: cat /var/lib/cwl/stgd090eb3d-8aaa-48e8-bc2c-2f5d38462115/OceanDNA-b40471.fa | prodigal -d OceanDNA-b40471/cds.fna -a OceanDNA-b40471/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:59:00,395] [INFO] Task succeeded: Prodigal
[2023-03-18 09:59:00,395] [INFO] Task started: HMMsearch
[2023-03-18 09:59:00,395] [INFO] Running command: hmmsearch --tblout OceanDNA-b40471/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2754e53-5fbd-4758-9696-aed79ec0ff06/dqc_reference/reference_markers.hmm OceanDNA-b40471/protein.faa > /dev/null
[2023-03-18 09:59:00,648] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:59:00,648] [INFO] Found 6/6 markers.
[2023-03-18 09:59:00,667] [INFO] Query marker FASTA was written to OceanDNA-b40471/markers.fasta
[2023-03-18 09:59:00,668] [INFO] Task started: Blastn
[2023-03-18 09:59:00,668] [INFO] Running command: blastn -query OceanDNA-b40471/markers.fasta -db /var/lib/cwl/stgf2754e53-5fbd-4758-9696-aed79ec0ff06/dqc_reference/reference_markers.fasta -out OceanDNA-b40471/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:01,373] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:01,373] [INFO] Selected 29 target genomes.
[2023-03-18 09:59:01,374] [INFO] Target genome list was writen to OceanDNA-b40471/target_genomes.txt
[2023-03-18 09:59:01,397] [INFO] Task started: fastANI
[2023-03-18 09:59:01,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgd090eb3d-8aaa-48e8-bc2c-2f5d38462115/OceanDNA-b40471.fa --refList OceanDNA-b40471/target_genomes.txt --output OceanDNA-b40471/fastani_result.tsv --threads 1
[2023-03-18 09:59:18,907] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:18,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2754e53-5fbd-4758-9696-aed79ec0ff06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:59:18,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2754e53-5fbd-4758-9696-aed79ec0ff06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:59:18,919] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:59:18,919] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:59:18,920] [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
Pseudohongiella acticola	strain=KCTC 42131	GCA_001758195.1	1524254	1524254	type	True	80.6324	682	1122	95	below_threshold
Pseudohongiella spirulinae	strain=KCTC 32221	GCA_001444425.1	1249552	1249552	type	True	77.6221	259	1122	95	below_threshold
Pseudohongiella nitratireducens	strain=CGMCC 1.15425	GCA_014642795.1	1768907	1768907	type	True	76.7565	142	1122	95	below_threshold
Pseudohongiella nitratireducens	strain=SCS-49	GCA_001642735.1	1768907	1768907	type	True	76.7389	148	1122	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	76.3292	51	1122	95	below_threshold
Pseudomonas fluvialis	strain=ASS-1	GCA_002234375.1	1793966	1793966	suspected-type	True	76.1819	62	1122	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	76.0959	69	1122	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	76.0588	69	1122	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	76.045	63	1122	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.0251	58	1122	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	76.0203	64	1122	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	76.0134	69	1122	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.0063	59	1122	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	75.9607	59	1122	95	below_threshold
Natronospirillum operosum	strain=G-116	GCA_004768465.1	2759953	2759953	type	True	75.8633	64	1122	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	75.8525	64	1122	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	75.8299	65	1122	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	75.8037	58	1122	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	75.7855	59	1122	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	75.4344	77	1122	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:59:18,920] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40471/tc_result.tsv
[2023-03-18 09:59:18,920] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:59:18,920] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:59:18,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2754e53-5fbd-4758-9696-aed79ec0ff06/dqc_reference/checkm_data
[2023-03-18 09:59:18,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:59:18,925] [INFO] Task started: CheckM
[2023-03-18 09:59:18,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40471/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40471/checkm_input OceanDNA-b40471/checkm_result
[2023-03-18 10:00:14,145] [INFO] Task succeeded: CheckM
[2023-03-18 10:00:14,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:00:14,148] [INFO] ===== Completeness check finished =====
[2023-03-18 10:00:14,148] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:00:14,148] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40471/markers.fasta)
[2023-03-18 10:00:14,149] [INFO] Task started: Blastn
[2023-03-18 10:00:14,149] [INFO] Running command: blastn -query OceanDNA-b40471/markers.fasta -db /var/lib/cwl/stgf2754e53-5fbd-4758-9696-aed79ec0ff06/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40471/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:00:15,358] [INFO] Task succeeded: Blastn
[2023-03-18 10:00:15,358] [INFO] Selected 14 target genomes.
[2023-03-18 10:00:15,359] [INFO] Target genome list was writen to OceanDNA-b40471/target_genomes_gtdb.txt
[2023-03-18 10:00:15,396] [INFO] Task started: fastANI
[2023-03-18 10:00:15,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgd090eb3d-8aaa-48e8-bc2c-2f5d38462115/OceanDNA-b40471.fa --refList OceanDNA-b40471/target_genomes_gtdb.txt --output OceanDNA-b40471/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:00:23,793] [INFO] Task succeeded: fastANI
[2023-03-18 10:00:23,800] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:00:23,801] [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_002711845.1	s__Pseudohongiella sp002711845	99.9987	1117	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCA_011050365.1	s__Pseudohongiella sp011050365	81.4891	777	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001758195.1	s__Pseudohongiella acticola	80.6324	682	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444425.1	s__Pseudohongiella spirulinae	77.6221	259	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354805.1	s__Pseudohongiella sp002354805	77.4322	293	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.49	99.10	0.99	0.98	3	-
GCA_002706685.1	s__Pseudohongiella sp002706685	77.3999	288	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.93	99.90	0.98	0.96	5	-
GCA_003556835.1	s__PWQG01 sp003556835	77.0226	145	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__PWQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004535785.1	s__Pseudohongiella sp004535785	76.9622	205	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802565.1	s__UBA5078 sp001802565	76.4456	107	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876785.1	s__UBA5078 sp903876785	76.189	81	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	99.18	99.13	0.80	0.78	4	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	76.0588	69	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
--------------------------------------------------------------------------------
[2023-03-18 10:00:23,801] [INFO] GTDB search result was written to OceanDNA-b40471/result_gtdb.tsv
[2023-03-18 10:00:23,801] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:00:23,803] [INFO] DFAST_QC result json was written to OceanDNA-b40471/dqc_result.json
[2023-03-18 10:00:23,803] [INFO] DFAST_QC completed!
[2023-03-18 10:00:23,803] [INFO] Total running time: 0h1m47s