[2023-03-17 00:45:47,089] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,089] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ae6b733-11d4-4320-b7af-fc0660cd57d3/dqc_reference
[2023-03-17 00:45:48,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,284] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,285] [INFO] Running command: cat /var/lib/cwl/stgf03f2e72-6393-4893-8d2a-b670dc20df26/OceanDNA-b40444.fa | prodigal -d OceanDNA-b40444/cds.fna -a OceanDNA-b40444/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:10,216] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:10,217] [INFO] Task started: HMMsearch
[2023-03-17 00:46:10,217] [INFO] Running command: hmmsearch --tblout OceanDNA-b40444/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ae6b733-11d4-4320-b7af-fc0660cd57d3/dqc_reference/reference_markers.hmm OceanDNA-b40444/protein.faa > /dev/null
[2023-03-17 00:46:10,433] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:10,434] [INFO] Found 6/6 markers.
[2023-03-17 00:46:10,455] [INFO] Query marker FASTA was written to OceanDNA-b40444/markers.fasta
[2023-03-17 00:46:10,456] [INFO] Task started: Blastn
[2023-03-17 00:46:10,456] [INFO] Running command: blastn -query OceanDNA-b40444/markers.fasta -db /var/lib/cwl/stg4ae6b733-11d4-4320-b7af-fc0660cd57d3/dqc_reference/reference_markers.fasta -out OceanDNA-b40444/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:11,161] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:11,161] [INFO] Selected 28 target genomes.
[2023-03-17 00:46:11,162] [INFO] Target genome list was writen to OceanDNA-b40444/target_genomes.txt
[2023-03-17 00:46:11,213] [INFO] Task started: fastANI
[2023-03-17 00:46:11,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgf03f2e72-6393-4893-8d2a-b670dc20df26/OceanDNA-b40444.fa --refList OceanDNA-b40444/target_genomes.txt --output OceanDNA-b40444/fastani_result.tsv --threads 1
[2023-03-17 00:46:29,107] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:29,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ae6b733-11d4-4320-b7af-fc0660cd57d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:29,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ae6b733-11d4-4320-b7af-fc0660cd57d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:29,119] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:29,119] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:46:29,119] [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	80.192	680	1142	95	below_threshold
Pseudohongiella spirulinae	strain=KCTC 32221	GCA_001444425.1	1249552	1249552	type	True	77.2806	270	1142	95	below_threshold
Pseudohongiella nitratireducens	strain=SCS-49	GCA_001642735.1	1768907	1768907	type	True	77.1196	126	1142	95	below_threshold
Pseudohongiella nitratireducens	strain=CGMCC 1.15425	GCA_014642795.1	1768907	1768907	type	True	77.0507	126	1142	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.7934	73	1142	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	75.7897	56	1142	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	75.7451	63	1142	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	75.7259	71	1142	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	75.7232	71	1142	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	75.7098	72	1142	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	75.7057	65	1142	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.6891	65	1142	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	75.654	60	1142	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	75.6161	60	1142	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.6081	67	1142	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.5816	61	1142	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	75.571	62	1142	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	75.4818	66	1142	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	75.3185	50	1142	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	75.3185	50	1142	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:29,119] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40444/tc_result.tsv
[2023-03-17 00:46:29,119] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:29,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:29,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ae6b733-11d4-4320-b7af-fc0660cd57d3/dqc_reference/checkm_data
[2023-03-17 00:46:29,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:29,125] [INFO] Task started: CheckM
[2023-03-17 00:46:29,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40444/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40444/checkm_input OceanDNA-b40444/checkm_result
[2023-03-17 00:47:24,083] [INFO] Task succeeded: CheckM
[2023-03-17 00:47:24,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:47:24,085] [INFO] ===== Completeness check finished =====
[2023-03-17 00:47:24,086] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:47:24,086] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40444/markers.fasta)
[2023-03-17 00:47:24,087] [INFO] Task started: Blastn
[2023-03-17 00:47:24,087] [INFO] Running command: blastn -query OceanDNA-b40444/markers.fasta -db /var/lib/cwl/stg4ae6b733-11d4-4320-b7af-fc0660cd57d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40444/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:47:25,270] [INFO] Task succeeded: Blastn
[2023-03-17 00:47:25,270] [INFO] Selected 13 target genomes.
[2023-03-17 00:47:25,270] [INFO] Target genome list was writen to OceanDNA-b40444/target_genomes_gtdb.txt
[2023-03-17 00:47:25,445] [INFO] Task started: fastANI
[2023-03-17 00:47:25,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgf03f2e72-6393-4893-8d2a-b670dc20df26/OceanDNA-b40444.fa --refList OceanDNA-b40444/target_genomes_gtdb.txt --output OceanDNA-b40444/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:33,723] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:33,730] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:47:33,731] [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	83.3524	853	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_011050365.1	s__Pseudohongiella sp011050365	81.4025	765	1142	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	80.1965	679	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706685.1	s__Pseudohongiella sp002706685	77.6156	278	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.93	99.90	0.98	0.96	5	-
GCA_002354805.1	s__Pseudohongiella sp002354805	77.3742	272	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.49	99.10	0.99	0.98	3	-
GCF_001444425.1	s__Pseudohongiella spirulinae	77.271	271	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642735.1	s__Pseudohongiella nitratireducens	77.1196	126	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.60	98.82	0.97	0.93	4	-
GCA_004535785.1	s__Pseudohongiella sp004535785	76.8761	184	1142	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	76.5744	99	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	75.7191	80	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_000689415.1	s__Pseudomonas knackmussii	75.571	62	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.27	98.27	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:33,731] [INFO] GTDB search result was written to OceanDNA-b40444/result_gtdb.tsv
[2023-03-17 00:47:33,731] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:33,732] [INFO] DFAST_QC result json was written to OceanDNA-b40444/dqc_result.json
[2023-03-17 00:47:33,733] [INFO] DFAST_QC completed!
[2023-03-17 00:47:33,733] [INFO] Total running time: 0h1m47s