[2023-03-15 15:56:48,643] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:56:48,643] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:56:48,643] [INFO] DQC Reference Directory: /var/lib/cwl/stgc627f4c7-1e53-4f8b-8332-88c1e5e094fb/dqc_reference
[2023-03-15 15:56:49,803] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:56:49,803] [INFO] Task started: Prodigal
[2023-03-15 15:56:49,803] [INFO] Running command: cat /var/lib/cwl/stged976ca0-21f5-41f7-9886-d2b7106aa955/OceanDNA-b34965.fa | prodigal -d OceanDNA-b34965/cds.fna -a OceanDNA-b34965/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:57:11,727] [INFO] Task succeeded: Prodigal
[2023-03-15 15:57:11,728] [INFO] Task started: HMMsearch
[2023-03-15 15:57:11,728] [INFO] Running command: hmmsearch --tblout OceanDNA-b34965/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc627f4c7-1e53-4f8b-8332-88c1e5e094fb/dqc_reference/reference_markers.hmm OceanDNA-b34965/protein.faa > /dev/null
[2023-03-15 15:57:11,965] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:57:11,965] [INFO] Found 6/6 markers.
[2023-03-15 15:57:11,991] [INFO] Query marker FASTA was written to OceanDNA-b34965/markers.fasta
[2023-03-15 15:57:11,992] [INFO] Task started: Blastn
[2023-03-15 15:57:11,992] [INFO] Running command: blastn -query OceanDNA-b34965/markers.fasta -db /var/lib/cwl/stgc627f4c7-1e53-4f8b-8332-88c1e5e094fb/dqc_reference/reference_markers.fasta -out OceanDNA-b34965/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:57:12,666] [INFO] Task succeeded: Blastn
[2023-03-15 15:57:12,667] [INFO] Selected 15 target genomes.
[2023-03-15 15:57:12,667] [INFO] Target genome list was writen to OceanDNA-b34965/target_genomes.txt
[2023-03-15 15:57:12,748] [INFO] Task started: fastANI
[2023-03-15 15:57:12,748] [INFO] Running command: fastANI --query /var/lib/cwl/stged976ca0-21f5-41f7-9886-d2b7106aa955/OceanDNA-b34965.fa --refList OceanDNA-b34965/target_genomes.txt --output OceanDNA-b34965/fastani_result.tsv --threads 1
[2023-03-15 15:57:25,346] [INFO] Task succeeded: fastANI
[2023-03-15 15:57:25,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc627f4c7-1e53-4f8b-8332-88c1e5e094fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:57:25,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc627f4c7-1e53-4f8b-8332-88c1e5e094fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:57:25,356] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:57:25,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:57:25,356] [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
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	87.5758	1137	1373	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	87.5163	1125	1373	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	86.0448	1010	1373	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	86.0279	1060	1373	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	85.9715	1046	1373	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	83.0284	983	1373	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	81.7567	727	1373	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	81.6655	730	1373	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	81.6513	737	1373	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	81.6185	706	1373	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	81.5238	753	1373	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.3106	566	1373	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.2629	78	1373	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.0369	75	1373	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:57:25,356] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34965/tc_result.tsv
[2023-03-15 15:57:25,356] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:57:25,356] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:57:25,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc627f4c7-1e53-4f8b-8332-88c1e5e094fb/dqc_reference/checkm_data
[2023-03-15 15:57:25,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:57:25,363] [INFO] Task started: CheckM
[2023-03-15 15:57:25,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34965/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34965/checkm_input OceanDNA-b34965/checkm_result
[2023-03-15 15:58:19,276] [INFO] Task succeeded: CheckM
[2023-03-15 15:58:19,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:58:19,279] [INFO] ===== Completeness check finished =====
[2023-03-15 15:58:19,279] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:58:19,279] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34965/markers.fasta)
[2023-03-15 15:58:19,280] [INFO] Task started: Blastn
[2023-03-15 15:58:19,280] [INFO] Running command: blastn -query OceanDNA-b34965/markers.fasta -db /var/lib/cwl/stgc627f4c7-1e53-4f8b-8332-88c1e5e094fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34965/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:58:20,325] [INFO] Task succeeded: Blastn
[2023-03-15 15:58:20,326] [INFO] Selected 9 target genomes.
[2023-03-15 15:58:20,326] [INFO] Target genome list was writen to OceanDNA-b34965/target_genomes_gtdb.txt
[2023-03-15 15:58:20,336] [INFO] Task started: fastANI
[2023-03-15 15:58:20,336] [INFO] Running command: fastANI --query /var/lib/cwl/stged976ca0-21f5-41f7-9886-d2b7106aa955/OceanDNA-b34965.fa --refList OceanDNA-b34965/target_genomes_gtdb.txt --output OceanDNA-b34965/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:58:29,660] [INFO] Task succeeded: fastANI
[2023-03-15 15:58:29,666] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:58:29,666] [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_007988745.1	s__Pseudoalteromonas atlantica	97.8902	1196	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	conclusive
GCF_001401805.1	s__Pseudoalteromonas sp001401805	92.6565	1176	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.16	97.37	0.91	0.90	5	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	87.5992	1135	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	86.014	1062	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	85.0683	963	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	82.7932	911	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000238275.3	s__Pseudoalteromonas undina	81.7644	726	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	81.6738	730	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	81.5856	692	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-15 15:58:29,667] [INFO] GTDB search result was written to OceanDNA-b34965/result_gtdb.tsv
[2023-03-15 15:58:29,667] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:58:29,668] [INFO] DFAST_QC result json was written to OceanDNA-b34965/dqc_result.json
[2023-03-15 15:58:29,668] [INFO] DFAST_QC completed!
[2023-03-15 15:58:29,668] [INFO] Total running time: 0h1m41s