[2023-03-15 18:39:12,305] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,305] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2724148-b2c0-40a6-bd80-8bfbd0e404de/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,658] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,658] [INFO] Running command: cat /var/lib/cwl/stg773f8946-b176-453b-ae7e-a811c5b36b60/OceanDNA-b23817.fa | prodigal -d OceanDNA-b23817/cds.fna -a OceanDNA-b23817/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:33,942] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:33,943] [INFO] Task started: HMMsearch
[2023-03-15 18:39:33,943] [INFO] Running command: hmmsearch --tblout OceanDNA-b23817/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2724148-b2c0-40a6-bd80-8bfbd0e404de/dqc_reference/reference_markers.hmm OceanDNA-b23817/protein.faa > /dev/null
[2023-03-15 18:39:34,139] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:34,139] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg773f8946-b176-453b-ae7e-a811c5b36b60/OceanDNA-b23817.fa]
[2023-03-15 18:39:34,161] [INFO] Query marker FASTA was written to OceanDNA-b23817/markers.fasta
[2023-03-15 18:39:34,161] [INFO] Task started: Blastn
[2023-03-15 18:39:34,161] [INFO] Running command: blastn -query OceanDNA-b23817/markers.fasta -db /var/lib/cwl/stgf2724148-b2c0-40a6-bd80-8bfbd0e404de/dqc_reference/reference_markers.fasta -out OceanDNA-b23817/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:34,754] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:34,755] [INFO] Selected 24 target genomes.
[2023-03-15 18:39:34,755] [INFO] Target genome list was writen to OceanDNA-b23817/target_genomes.txt
[2023-03-15 18:39:34,769] [INFO] Task started: fastANI
[2023-03-15 18:39:34,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg773f8946-b176-453b-ae7e-a811c5b36b60/OceanDNA-b23817.fa --refList OceanDNA-b23817/target_genomes.txt --output OceanDNA-b23817/fastani_result.tsv --threads 1
[2023-03-15 18:39:50,356] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:50,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2724148-b2c0-40a6-bd80-8bfbd0e404de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:50,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2724148-b2c0-40a6-bd80-8bfbd0e404de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:50,362] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:50,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:39:50,362] [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
Ponticaulis koreensis	strain=DSM 19734	GCA_000420665.1	1123045	1123045	type	True	92.1272	977	1107	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	76.4625	67	1107	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	76.0689	76	1107	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.0426	77	1107	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	75.8393	76	1107	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	75.6251	62	1107	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	75.454	55	1107	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:39:50,362] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23817/tc_result.tsv
[2023-03-15 18:39:50,362] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:50,362] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:50,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2724148-b2c0-40a6-bd80-8bfbd0e404de/dqc_reference/checkm_data
[2023-03-15 18:39:50,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:50,367] [INFO] Task started: CheckM
[2023-03-15 18:39:50,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23817/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23817/checkm_input OceanDNA-b23817/checkm_result
[2023-03-15 18:40:41,828] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:41,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:41,831] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:41,831] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:41,831] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23817/markers.fasta)
[2023-03-15 18:40:41,831] [INFO] Task started: Blastn
[2023-03-15 18:40:41,831] [INFO] Running command: blastn -query OceanDNA-b23817/markers.fasta -db /var/lib/cwl/stgf2724148-b2c0-40a6-bd80-8bfbd0e404de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23817/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:42,808] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:42,808] [INFO] Selected 10 target genomes.
[2023-03-15 18:40:42,808] [INFO] Target genome list was writen to OceanDNA-b23817/target_genomes_gtdb.txt
[2023-03-15 18:40:43,013] [INFO] Task started: fastANI
[2023-03-15 18:40:43,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg773f8946-b176-453b-ae7e-a811c5b36b60/OceanDNA-b23817.fa --refList OceanDNA-b23817/target_genomes_gtdb.txt --output OceanDNA-b23817/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:50,574] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:50,580] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:40:50,580] [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_002338565.1	s__Ponticaulis sp002338565	99.9792	1077	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.94	99.86	0.98	0.96	4	conclusive
GCA_002723155.1	s__Ponticaulis sp002723155	92.9504	969	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.28	99.28	0.86	0.86	2	-
GCF_000420665.1	s__Ponticaulis koreensis	92.1148	978	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002173095.1	s__Ponticaulis sp002173095	80.2005	459	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002701295.1	s__Ponticaulis sp002701295	77.817	238	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692725.1	s__Ponticaulis sp002692725	77.3087	254	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699325.1	s__Ponticaulis sp002699325	77.2826	206	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682675.1	s__Hyphomonas pacifica	75.6251	62	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:50,580] [INFO] GTDB search result was written to OceanDNA-b23817/result_gtdb.tsv
[2023-03-15 18:40:50,580] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:50,581] [INFO] DFAST_QC result json was written to OceanDNA-b23817/dqc_result.json
[2023-03-15 18:40:50,581] [INFO] DFAST_QC completed!
[2023-03-15 18:40:50,581] [INFO] Total running time: 0h1m38s