[2023-03-19 01:25:20,234] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:25:20,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:25:20,234] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2163e11-b0c7-41af-99e8-f41469e88384/dqc_reference
[2023-03-19 01:25:21,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:25:21,311] [INFO] Task started: Prodigal
[2023-03-19 01:25:21,311] [INFO] Running command: cat /var/lib/cwl/stgc1c5e095-5a02-45be-b0cd-5e38d13d231e/OceanDNA-b23175.fa | prodigal -d OceanDNA-b23175/cds.fna -a OceanDNA-b23175/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:25:55,763] [INFO] Task succeeded: Prodigal
[2023-03-19 01:25:55,763] [INFO] Task started: HMMsearch
[2023-03-19 01:25:55,763] [INFO] Running command: hmmsearch --tblout OceanDNA-b23175/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2163e11-b0c7-41af-99e8-f41469e88384/dqc_reference/reference_markers.hmm OceanDNA-b23175/protein.faa > /dev/null
[2023-03-19 01:25:56,050] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:25:56,051] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc1c5e095-5a02-45be-b0cd-5e38d13d231e/OceanDNA-b23175.fa]
[2023-03-19 01:25:56,102] [INFO] Query marker FASTA was written to OceanDNA-b23175/markers.fasta
[2023-03-19 01:25:56,103] [INFO] Task started: Blastn
[2023-03-19 01:25:56,103] [INFO] Running command: blastn -query OceanDNA-b23175/markers.fasta -db /var/lib/cwl/stgb2163e11-b0c7-41af-99e8-f41469e88384/dqc_reference/reference_markers.fasta -out OceanDNA-b23175/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:25:56,650] [INFO] Task succeeded: Blastn
[2023-03-19 01:25:56,653] [INFO] Selected 22 target genomes.
[2023-03-19 01:25:56,653] [INFO] Target genome list was writen to OceanDNA-b23175/target_genomes.txt
[2023-03-19 01:25:56,667] [INFO] Task started: fastANI
[2023-03-19 01:25:56,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1c5e095-5a02-45be-b0cd-5e38d13d231e/OceanDNA-b23175.fa --refList OceanDNA-b23175/target_genomes.txt --output OceanDNA-b23175/fastani_result.tsv --threads 1
[2023-03-19 01:26:16,644] [INFO] Task succeeded: fastANI
[2023-03-19 01:26:16,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2163e11-b0c7-41af-99e8-f41469e88384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:26:16,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2163e11-b0c7-41af-99e8-f41469e88384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:26:16,656] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:26:16,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:26:16,656] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.0265	59	1991	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	74.8711	86	1991	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8171	167	1991	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.8096	85	1991	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.7659	106	1991	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7268	195	1991	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	74.692	90	1991	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.6701	92	1991	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	74.6611	151	1991	95	below_threshold
Microbacterium marinum	strain=DSM 24947	GCA_014204835.1	421115	421115	type	True	74.6576	55	1991	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	74.6438	138	1991	95	below_threshold
Kineococcus rhizosphaerae	strain=DSM 19711	GCA_003002055.1	559628	559628	type	True	74.6391	139	1991	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	74.6345	149	1991	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	74.6338	150	1991	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	74.6327	151	1991	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	74.6198	122	1991	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	74.5885	90	1991	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	74.5684	103	1991	95	below_threshold
Streptomyces recifensis	strain=NRRL B-3811	GCA_002154615.1	67355	67355	type	True	74.5671	70	1991	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:26:16,656] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23175/tc_result.tsv
[2023-03-19 01:26:16,656] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:26:16,656] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:26:16,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2163e11-b0c7-41af-99e8-f41469e88384/dqc_reference/checkm_data
[2023-03-19 01:26:16,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:26:16,668] [INFO] Task started: CheckM
[2023-03-19 01:26:16,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23175/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23175/checkm_input OceanDNA-b23175/checkm_result
[2023-03-19 01:27:37,508] [INFO] Task succeeded: CheckM
[2023-03-19 01:27:37,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.48%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-19 01:27:37,513] [INFO] ===== Completeness check finished =====
[2023-03-19 01:27:37,513] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:27:37,513] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23175/markers.fasta)
[2023-03-19 01:27:37,514] [INFO] Task started: Blastn
[2023-03-19 01:27:37,514] [INFO] Running command: blastn -query OceanDNA-b23175/markers.fasta -db /var/lib/cwl/stgb2163e11-b0c7-41af-99e8-f41469e88384/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23175/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:27:38,265] [INFO] Task succeeded: Blastn
[2023-03-19 01:27:38,266] [INFO] Selected 19 target genomes.
[2023-03-19 01:27:38,266] [INFO] Target genome list was writen to OceanDNA-b23175/target_genomes_gtdb.txt
[2023-03-19 01:27:38,287] [INFO] Task started: fastANI
[2023-03-19 01:27:38,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1c5e095-5a02-45be-b0cd-5e38d13d231e/OceanDNA-b23175.fa --refList OceanDNA-b23175/target_genomes_gtdb.txt --output OceanDNA-b23175/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:27:56,044] [INFO] Task succeeded: fastANI
[2023-03-19 01:27:56,054] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:27:56,054] [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_016765095.1	s__NORP233 sp016765095	79.8008	903	1991	d__Bacteria;p__Planctomycetota;c__J058;o__J058;f__J058;g__NORP233	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695705.1	s__J058 sp003695705	75.9015	342	1991	d__Bacteria;p__Planctomycetota;c__J058;o__J058;f__J058;g__J058	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873195.1	s__VGXW01 sp016873195	75.029	104	1991	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872675.1	s__UBA2386 sp016872675	74.8802	97	1991	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794565.1	s__JAEUHS01 sp016794565	74.816	83	1991	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	74.8144	50	1991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_016653355.1	s__Rhodoplanes elegans	74.7629	106	1991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCA_014647935.1	s__Planomonospora parontospora	74.6756	140	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCA_004297725.1	s__SCUS01 sp004297725	74.6749	207	1991	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__SCUS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	74.6436	139	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_015711645.1	s__Planomonospora sp015711645	74.6181	140	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015350975.1	s__Curtobacterium sp015350975	74.6175	73	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715785.1	s__Streptomyces puniciscabiei	74.6153	123	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.70	95.42	0.91	0.82	3	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	74.6139	144	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744495.1	s__Caulobacter sp017744495	74.6045	56	1991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989515.1	s__Curtobacterium sp003989515	74.5549	61	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.86	98.78	0.96	0.96	3	-
GCF_019038435.1	s__Nocardia sp019038435	74.545	89	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:27:56,055] [INFO] GTDB search result was written to OceanDNA-b23175/result_gtdb.tsv
[2023-03-19 01:27:56,055] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:27:56,057] [INFO] DFAST_QC result json was written to OceanDNA-b23175/dqc_result.json
[2023-03-19 01:27:56,057] [INFO] DFAST_QC completed!
[2023-03-19 01:27:56,057] [INFO] Total running time: 0h2m36s