[2023-03-15 06:19:32,786] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:19:32,786] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:19:32,786] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbcda515-44e1-4f10-b596-0da4c73eeb2b/dqc_reference
[2023-03-15 06:19:34,567] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:19:34,567] [INFO] Task started: Prodigal
[2023-03-15 06:19:34,567] [INFO] Running command: cat /var/lib/cwl/stg52ca53c5-7892-4a57-9a16-244134713961/OceanDNA-b38870.fa | prodigal -d OceanDNA-b38870/cds.fna -a OceanDNA-b38870/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:19:54,510] [INFO] Task succeeded: Prodigal
[2023-03-15 06:19:54,511] [INFO] Task started: HMMsearch
[2023-03-15 06:19:54,511] [INFO] Running command: hmmsearch --tblout OceanDNA-b38870/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbcda515-44e1-4f10-b596-0da4c73eeb2b/dqc_reference/reference_markers.hmm OceanDNA-b38870/protein.faa > /dev/null
[2023-03-15 06:19:54,723] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:19:54,724] [INFO] Found 6/6 markers.
[2023-03-15 06:19:54,746] [INFO] Query marker FASTA was written to OceanDNA-b38870/markers.fasta
[2023-03-15 06:19:54,747] [INFO] Task started: Blastn
[2023-03-15 06:19:54,747] [INFO] Running command: blastn -query OceanDNA-b38870/markers.fasta -db /var/lib/cwl/stgfbcda515-44e1-4f10-b596-0da4c73eeb2b/dqc_reference/reference_markers.fasta -out OceanDNA-b38870/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:19:55,358] [INFO] Task succeeded: Blastn
[2023-03-15 06:19:55,359] [INFO] Selected 28 target genomes.
[2023-03-15 06:19:55,359] [INFO] Target genome list was writen to OceanDNA-b38870/target_genomes.txt
[2023-03-15 06:19:55,375] [INFO] Task started: fastANI
[2023-03-15 06:19:55,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg52ca53c5-7892-4a57-9a16-244134713961/OceanDNA-b38870.fa --refList OceanDNA-b38870/target_genomes.txt --output OceanDNA-b38870/fastani_result.tsv --threads 1
[2023-03-15 06:20:13,367] [INFO] Task succeeded: fastANI
[2023-03-15 06:20:13,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbcda515-44e1-4f10-b596-0da4c73eeb2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:20:13,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbcda515-44e1-4f10-b596-0da4c73eeb2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:20:13,377] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:20:13,377] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:20:13,377] [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
Motiliproteus sediminis	strain=HS6	GCA_017912535.1	1468178	1468178	type	True	77.7379	147	1123	95	below_threshold
Motiliproteus coralliicola	strain=C34	GCA_003345655.1	2283196	2283196	type	True	77.7288	234	1123	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	76.7901	73	1123	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.597	110	1123	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	76.3795	95	1123	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	76.3509	57	1123	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	76.3347	54	1123	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	76.2718	76	1123	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	76.2112	86	1123	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	76.1148	77	1123	95	below_threshold
Aestuariirhabdus litorea	strain=GTF13	GCA_003864255.1	2528527	2528527	type	True	75.982	64	1123	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.7785	50	1123	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.6312	51	1123	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:20:13,377] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38870/tc_result.tsv
[2023-03-15 06:20:13,378] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:20:13,378] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:20:13,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbcda515-44e1-4f10-b596-0da4c73eeb2b/dqc_reference/checkm_data
[2023-03-15 06:20:13,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:20:13,384] [INFO] Task started: CheckM
[2023-03-15 06:20:13,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38870/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38870/checkm_input OceanDNA-b38870/checkm_result
[2023-03-15 06:21:03,154] [INFO] Task succeeded: CheckM
[2023-03-15 06:21:03,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 06:21:03,192] [INFO] ===== Completeness check finished =====
[2023-03-15 06:21:03,192] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:21:03,193] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38870/markers.fasta)
[2023-03-15 06:21:03,194] [INFO] Task started: Blastn
[2023-03-15 06:21:03,194] [INFO] Running command: blastn -query OceanDNA-b38870/markers.fasta -db /var/lib/cwl/stgfbcda515-44e1-4f10-b596-0da4c73eeb2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38870/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:21:04,173] [INFO] Task succeeded: Blastn
[2023-03-15 06:21:04,174] [INFO] Selected 23 target genomes.
[2023-03-15 06:21:04,174] [INFO] Target genome list was writen to OceanDNA-b38870/target_genomes_gtdb.txt
[2023-03-15 06:21:04,202] [INFO] Task started: fastANI
[2023-03-15 06:21:04,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg52ca53c5-7892-4a57-9a16-244134713961/OceanDNA-b38870.fa --refList OceanDNA-b38870/target_genomes_gtdb.txt --output OceanDNA-b38870/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:21:19,081] [INFO] Task succeeded: fastANI
[2023-03-15 06:21:19,089] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:21:19,089] [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_004195305.1	s__Motiliproteus sp004195305	80.1684	359	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017912535.1	s__Motiliproteus sediminis	77.7379	147	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345655.1	s__Motiliproteus coralliicola	77.7147	235	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309075.1	s__Motiliproteus sp017309075	77.2117	169	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250495.1	s__Marinobacterium sp003250495	76.9195	69	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108065.1	s__Marinobacterium lutimaris	76.7608	74	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	76.4235	95	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051665.1	s__Amphritea spongicola	76.3509	57	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107855.1	s__Marinobacterium georgiense	76.3347	54	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.23	97.23	0.75	0.75	2	-
GCA_013373085.1	s__Marinobacterium_A sp013373085	76.2926	88	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641945.1	s__Marinobacterium zhoushanense	76.2598	86	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003864255.1	s__Aestuariirhabdus litorea	75.994	65	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Aestuariirhabdaceae;g__Aestuariirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 06:21:19,089] [INFO] GTDB search result was written to OceanDNA-b38870/result_gtdb.tsv
[2023-03-15 06:21:19,089] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:21:19,091] [INFO] DFAST_QC result json was written to OceanDNA-b38870/dqc_result.json
[2023-03-15 06:21:19,091] [INFO] DFAST_QC completed!
[2023-03-15 06:21:19,091] [INFO] Total running time: 0h1m46s