[2023-03-15 23:42:29,665] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,665] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,665] [INFO] DQC Reference Directory: /var/lib/cwl/stge362edad-4533-44bb-a660-16fc9e9b775c/dqc_reference
[2023-03-15 23:42:31,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,275] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,275] [INFO] Running command: cat /var/lib/cwl/stg640785b6-47a4-41e3-8b5c-a7c737710b1f/OceanDNA-b29532.fa | prodigal -d OceanDNA-b29532/cds.fna -a OceanDNA-b29532/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:55,212] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:55,213] [INFO] Task started: HMMsearch
[2023-03-15 23:42:55,213] [INFO] Running command: hmmsearch --tblout OceanDNA-b29532/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge362edad-4533-44bb-a660-16fc9e9b775c/dqc_reference/reference_markers.hmm OceanDNA-b29532/protein.faa > /dev/null
[2023-03-15 23:42:55,412] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:55,413] [INFO] Found 6/6 markers.
[2023-03-15 23:42:55,436] [INFO] Query marker FASTA was written to OceanDNA-b29532/markers.fasta
[2023-03-15 23:42:55,436] [INFO] Task started: Blastn
[2023-03-15 23:42:55,436] [INFO] Running command: blastn -query OceanDNA-b29532/markers.fasta -db /var/lib/cwl/stge362edad-4533-44bb-a660-16fc9e9b775c/dqc_reference/reference_markers.fasta -out OceanDNA-b29532/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:56,199] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:56,200] [INFO] Selected 21 target genomes.
[2023-03-15 23:42:56,200] [INFO] Target genome list was writen to OceanDNA-b29532/target_genomes.txt
[2023-03-15 23:42:56,214] [INFO] Task started: fastANI
[2023-03-15 23:42:56,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg640785b6-47a4-41e3-8b5c-a7c737710b1f/OceanDNA-b29532.fa --refList OceanDNA-b29532/target_genomes.txt --output OceanDNA-b29532/fastani_result.tsv --threads 1
[2023-03-15 23:43:13,037] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:13,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge362edad-4533-44bb-a660-16fc9e9b775c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:43:13,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge362edad-4533-44bb-a660-16fc9e9b775c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:43:13,049] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:43:13,049] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:43:13,049] [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
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	83.1898	882	1269	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	83.1041	900	1269	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	83.0818	900	1269	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	82.4758	820	1269	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.1925	407	1269	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.9323	380	1269	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.8974	322	1269	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.6451	319	1269	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	77.6414	370	1269	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.6233	319	1269	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.4823	258	1269	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.4391	228	1269	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.2159	292	1269	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.0546	248	1269	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.0434	247	1269	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.7901	204	1269	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	76.0019	69	1269	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.6464	79	1269	95	below_threshold
Actinopolymorpha pittospori	strain=DSM 45354	GCA_014873875.1	648752	648752	type	True	74.6041	59	1269	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:43:13,049] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29532/tc_result.tsv
[2023-03-15 23:43:13,050] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:43:13,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:43:13,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge362edad-4533-44bb-a660-16fc9e9b775c/dqc_reference/checkm_data
[2023-03-15 23:43:13,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:43:13,062] [INFO] Task started: CheckM
[2023-03-15 23:43:13,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29532/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29532/checkm_input OceanDNA-b29532/checkm_result
[2023-03-15 23:44:14,286] [INFO] Task succeeded: CheckM
[2023-03-15 23:44:14,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:44:14,291] [INFO] ===== Completeness check finished =====
[2023-03-15 23:44:14,292] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:44:14,292] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29532/markers.fasta)
[2023-03-15 23:44:14,293] [INFO] Task started: Blastn
[2023-03-15 23:44:14,293] [INFO] Running command: blastn -query OceanDNA-b29532/markers.fasta -db /var/lib/cwl/stge362edad-4533-44bb-a660-16fc9e9b775c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29532/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:44:15,718] [INFO] Task succeeded: Blastn
[2023-03-15 23:44:15,719] [INFO] Selected 13 target genomes.
[2023-03-15 23:44:15,719] [INFO] Target genome list was writen to OceanDNA-b29532/target_genomes_gtdb.txt
[2023-03-15 23:44:15,732] [INFO] Task started: fastANI
[2023-03-15 23:44:15,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg640785b6-47a4-41e3-8b5c-a7c737710b1f/OceanDNA-b29532.fa --refList OceanDNA-b29532/target_genomes_gtdb.txt --output OceanDNA-b29532/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:44:25,110] [INFO] Task succeeded: fastANI
[2023-03-15 23:44:25,118] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:44:25,118] [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_002695005.1	s__Maritimibacter sp002695005	99.9963	1259	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000152805.1	s__Maritimibacter alkaliphilus	83.0818	900	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	-
GCF_009882975.1	s__Maritimibacter harenae	82.467	821	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218265.1	s__Maritimibacter sp019218265	80.2604	645	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218295.1	s__Maritimibacter sp019218295	79.9207	633	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520545.1	s__Maritimibacter sp003520545	79.7439	495	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389895.1	s__Maritimibacter sp011389895	79.3889	562	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640115.1	s__Muriiphilus lacisalsi	79.0216	502	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.0453	246	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	76.0019	69	1269	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424625.1	s__Baekduia woesei_A	74.9227	82	1269	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:44:25,118] [INFO] GTDB search result was written to OceanDNA-b29532/result_gtdb.tsv
[2023-03-15 23:44:25,119] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:44:25,121] [INFO] DFAST_QC result json was written to OceanDNA-b29532/dqc_result.json
[2023-03-15 23:44:25,121] [INFO] DFAST_QC completed!
[2023-03-15 23:44:25,121] [INFO] Total running time: 0h1m55s