[2023-03-16 23:35:12,969] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,969] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c541d41-36cb-46ba-9592-c3429aa66f2f/dqc_reference
[2023-03-16 23:35:14,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,100] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stgacfc138f-3ef2-4c54-8767-6bac1fa42ccd/OceanDNA-b26770.fa | prodigal -d OceanDNA-b26770/cds.fna -a OceanDNA-b26770/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:22,358] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:22,358] [INFO] Task started: HMMsearch
[2023-03-16 23:35:22,359] [INFO] Running command: hmmsearch --tblout OceanDNA-b26770/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c541d41-36cb-46ba-9592-c3429aa66f2f/dqc_reference/reference_markers.hmm OceanDNA-b26770/protein.faa > /dev/null
[2023-03-16 23:35:22,507] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:22,508] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgacfc138f-3ef2-4c54-8767-6bac1fa42ccd/OceanDNA-b26770.fa]
[2023-03-16 23:35:22,520] [INFO] Query marker FASTA was written to OceanDNA-b26770/markers.fasta
[2023-03-16 23:35:22,520] [INFO] Task started: Blastn
[2023-03-16 23:35:22,520] [INFO] Running command: blastn -query OceanDNA-b26770/markers.fasta -db /var/lib/cwl/stg1c541d41-36cb-46ba-9592-c3429aa66f2f/dqc_reference/reference_markers.fasta -out OceanDNA-b26770/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:23,079] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:23,080] [INFO] Selected 14 target genomes.
[2023-03-16 23:35:23,080] [INFO] Target genome list was writen to OceanDNA-b26770/target_genomes.txt
[2023-03-16 23:35:23,089] [INFO] Task started: fastANI
[2023-03-16 23:35:23,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgacfc138f-3ef2-4c54-8767-6bac1fa42ccd/OceanDNA-b26770.fa --refList OceanDNA-b26770/target_genomes.txt --output OceanDNA-b26770/fastani_result.tsv --threads 1
[2023-03-16 23:35:33,653] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:33,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c541d41-36cb-46ba-9592-c3429aa66f2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:33,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c541d41-36cb-46ba-9592-c3429aa66f2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:33,662] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:33,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:35:33,663] [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
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	77.1025	176	459	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.9857	176	459	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	76.8978	138	459	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.8693	181	459	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.85	170	459	95	below_threshold
Pararhizobium mangrovi	strain=BGMRC 6574	GCA_006516965.1	2590452	2590452	type	True	76.8219	136	459	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	76.6926	124	459	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.6523	198	459	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.4586	116	459	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	76.4427	132	459	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	76.4306	133	459	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	76.4022	133	459	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.2888	172	459	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	76.0039	123	459	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:35:33,663] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26770/tc_result.tsv
[2023-03-16 23:35:33,663] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:33,663] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:33,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c541d41-36cb-46ba-9592-c3429aa66f2f/dqc_reference/checkm_data
[2023-03-16 23:35:33,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:33,667] [INFO] Task started: CheckM
[2023-03-16 23:35:33,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26770/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26770/checkm_input OceanDNA-b26770/checkm_result
[2023-03-16 23:35:58,263] [INFO] Task succeeded: CheckM
[2023-03-16 23:35:58,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:35:58,266] [INFO] ===== Completeness check finished =====
[2023-03-16 23:35:58,266] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:35:58,266] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26770/markers.fasta)
[2023-03-16 23:35:58,266] [INFO] Task started: Blastn
[2023-03-16 23:35:58,266] [INFO] Running command: blastn -query OceanDNA-b26770/markers.fasta -db /var/lib/cwl/stg1c541d41-36cb-46ba-9592-c3429aa66f2f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26770/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:59,115] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:59,116] [INFO] Selected 14 target genomes.
[2023-03-16 23:35:59,116] [INFO] Target genome list was writen to OceanDNA-b26770/target_genomes_gtdb.txt
[2023-03-16 23:35:59,259] [INFO] Task started: fastANI
[2023-03-16 23:35:59,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgacfc138f-3ef2-4c54-8767-6bac1fa42ccd/OceanDNA-b26770.fa --refList OceanDNA-b26770/target_genomes_gtdb.txt --output OceanDNA-b26770/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:36:09,546] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:09,556] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:36:09,556] [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_017305835.1	s__RCIO01 sp017305835	77.553	215	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	77.4956	182	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331955.1	s__Roseitalea porphyridii	77.3494	150	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	76.8556	182	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583935.1	s__Aureimonas flava	76.7901	166	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	76.7848	158	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	76.6922	171	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	76.6903	134	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	76.6744	197	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_014636935.1	s__Alsobacter metallidurans	76.4488	130	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	76.4306	133	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	76.3736	164	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455965.1	s__Methylobacterium sp001455965	76.0636	112	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693835.1	s__Rubrimonas sp007693835	76.0389	113	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:36:09,557] [INFO] GTDB search result was written to OceanDNA-b26770/result_gtdb.tsv
[2023-03-16 23:36:09,557] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:36:09,558] [INFO] DFAST_QC result json was written to OceanDNA-b26770/dqc_result.json
[2023-03-16 23:36:09,559] [INFO] DFAST_QC completed!
[2023-03-16 23:36:09,559] [INFO] Total running time: 0h0m57s