[2023-03-15 21:24:36,468] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgcaadc726-d89d-4226-8713-eb2aedecfab2/dqc_reference
[2023-03-15 21:24:37,602] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,602] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,602] [INFO] Running command: cat /var/lib/cwl/stg15cfdf27-4b53-4ac2-8825-853b02c94311/OceanDNA-b35152.fa | prodigal -d OceanDNA-b35152/cds.fna -a OceanDNA-b35152/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:25:04,095] [INFO] Task succeeded: Prodigal
[2023-03-15 21:25:04,095] [INFO] Task started: HMMsearch
[2023-03-15 21:25:04,095] [INFO] Running command: hmmsearch --tblout OceanDNA-b35152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcaadc726-d89d-4226-8713-eb2aedecfab2/dqc_reference/reference_markers.hmm OceanDNA-b35152/protein.faa > /dev/null
[2023-03-15 21:25:04,314] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:25:04,315] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg15cfdf27-4b53-4ac2-8825-853b02c94311/OceanDNA-b35152.fa]
[2023-03-15 21:25:04,342] [INFO] Query marker FASTA was written to OceanDNA-b35152/markers.fasta
[2023-03-15 21:25:04,343] [INFO] Task started: Blastn
[2023-03-15 21:25:04,343] [INFO] Running command: blastn -query OceanDNA-b35152/markers.fasta -db /var/lib/cwl/stgcaadc726-d89d-4226-8713-eb2aedecfab2/dqc_reference/reference_markers.fasta -out OceanDNA-b35152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:05,142] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:05,143] [INFO] Selected 11 target genomes.
[2023-03-15 21:25:05,144] [INFO] Target genome list was writen to OceanDNA-b35152/target_genomes.txt
[2023-03-15 21:25:05,150] [INFO] Task started: fastANI
[2023-03-15 21:25:05,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg15cfdf27-4b53-4ac2-8825-853b02c94311/OceanDNA-b35152.fa --refList OceanDNA-b35152/target_genomes.txt --output OceanDNA-b35152/fastani_result.tsv --threads 1
[2023-03-15 21:25:15,629] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:15,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcaadc726-d89d-4226-8713-eb2aedecfab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:25:15,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcaadc726-d89d-4226-8713-eb2aedecfab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:25:15,637] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 21:25:15,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 21:25:15,638] [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
Pantoea agglomerans	strain=FDAARGOS 1447	GCA_019048385.1	549	549	suspected-type	True	96.9116	1110	1485	95	conclusive
Pantoea agglomerans	strain=NBRC 102470	GCA_001598475.1	549	549	suspected-type	True	96.877	1107	1485	95	conclusive
Pantoea eucalypti	strain=LMG 24197	GCA_009646115.1	470933	470933	type	True	89.8327	1018	1485	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_006494355.1	470933	470933	type	True	89.8117	998	1485	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	87.6942	961	1485	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	87.6002	865	1485	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	85.7867	840	1485	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	80.6267	645	1485	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.1645	399	1485	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.1509	372	1485	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.035	392	1485	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:25:15,638] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35152/tc_result.tsv
[2023-03-15 21:25:15,638] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:25:15,638] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:25:15,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcaadc726-d89d-4226-8713-eb2aedecfab2/dqc_reference/checkm_data
[2023-03-15 21:25:15,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:25:15,651] [INFO] Task started: CheckM
[2023-03-15 21:25:15,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35152/checkm_input OceanDNA-b35152/checkm_result
[2023-03-15 21:26:21,052] [INFO] Task succeeded: CheckM
[2023-03-15 21:26:21,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:26:21,055] [INFO] ===== Completeness check finished =====
[2023-03-15 21:26:21,055] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:26:21,056] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35152/markers.fasta)
[2023-03-15 21:26:21,057] [INFO] Task started: Blastn
[2023-03-15 21:26:21,057] [INFO] Running command: blastn -query OceanDNA-b35152/markers.fasta -db /var/lib/cwl/stgcaadc726-d89d-4226-8713-eb2aedecfab2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:26:22,355] [INFO] Task succeeded: Blastn
[2023-03-15 21:26:22,356] [INFO] Selected 7 target genomes.
[2023-03-15 21:26:22,356] [INFO] Target genome list was writen to OceanDNA-b35152/target_genomes_gtdb.txt
[2023-03-15 21:26:22,514] [INFO] Task started: fastANI
[2023-03-15 21:26:22,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg15cfdf27-4b53-4ac2-8825-853b02c94311/OceanDNA-b35152.fa --refList OceanDNA-b35152/target_genomes_gtdb.txt --output OceanDNA-b35152/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:26:30,409] [INFO] Task succeeded: fastANI
[2023-03-15 21:26:30,415] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:26:30,415] [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_001598475.1	s__Pantoea agglomerans	96.877	1107	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.21	96.93	0.94	0.88	124	conclusive
GCF_900115075.1	s__Pantoea sp900115075	91.5206	1071	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.06	96.06	0.92	0.92	2	-
GCF_009905795.1	s__Pantoea sp003512445	90.8275	995	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.25	99.25	0.92	0.92	2	-
GCF_013415305.1	s__Pantoea sp002419935	90.5734	1027	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.92	98.92	0.97	0.97	2	-
GCF_004792415.1	s__Pantoea vagans	90.38	1052	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.00	95.86	0.91	0.88	14	-
GCF_008632075.1	s__Pantoea sp008632075	89.9083	1005	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.47	99.36	0.95	0.94	34	-
GCF_009646115.1	s__Pantoea eucalypti	89.8327	1018	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.21	98.96	0.95	0.93	16	-
--------------------------------------------------------------------------------
[2023-03-15 21:26:30,415] [INFO] GTDB search result was written to OceanDNA-b35152/result_gtdb.tsv
[2023-03-15 21:26:30,415] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:26:30,416] [INFO] DFAST_QC result json was written to OceanDNA-b35152/dqc_result.json
[2023-03-15 21:26:30,416] [INFO] DFAST_QC completed!
[2023-03-15 21:26:30,416] [INFO] Total running time: 0h1m54s