[2023-03-19 01:38:53,903] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,903] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg4409ddcf-6d2b-4309-937d-4b45131e6d54/dqc_reference
[2023-03-19 01:38:55,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:55,010] [INFO] Task started: Prodigal
[2023-03-19 01:38:55,010] [INFO] Running command: cat /var/lib/cwl/stgd4b1ac60-47fb-44e3-901b-de3c0698ff9f/OceanDNA-b23515.fa | prodigal -d OceanDNA-b23515/cds.fna -a OceanDNA-b23515/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:39:07,607] [INFO] Task succeeded: Prodigal
[2023-03-19 01:39:07,608] [INFO] Task started: HMMsearch
[2023-03-19 01:39:07,608] [INFO] Running command: hmmsearch --tblout OceanDNA-b23515/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4409ddcf-6d2b-4309-937d-4b45131e6d54/dqc_reference/reference_markers.hmm OceanDNA-b23515/protein.faa > /dev/null
[2023-03-19 01:39:07,777] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:39:07,778] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd4b1ac60-47fb-44e3-901b-de3c0698ff9f/OceanDNA-b23515.fa]
[2023-03-19 01:39:07,804] [INFO] Query marker FASTA was written to OceanDNA-b23515/markers.fasta
[2023-03-19 01:39:07,804] [INFO] Task started: Blastn
[2023-03-19 01:39:07,804] [INFO] Running command: blastn -query OceanDNA-b23515/markers.fasta -db /var/lib/cwl/stg4409ddcf-6d2b-4309-937d-4b45131e6d54/dqc_reference/reference_markers.fasta -out OceanDNA-b23515/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:08,419] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:08,420] [INFO] Selected 24 target genomes.
[2023-03-19 01:39:08,421] [INFO] Target genome list was writen to OceanDNA-b23515/target_genomes.txt
[2023-03-19 01:39:08,438] [INFO] Task started: fastANI
[2023-03-19 01:39:08,438] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b1ac60-47fb-44e3-901b-de3c0698ff9f/OceanDNA-b23515.fa --refList OceanDNA-b23515/target_genomes.txt --output OceanDNA-b23515/fastani_result.tsv --threads 1
[2023-03-19 01:39:22,933] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:22,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4409ddcf-6d2b-4309-937d-4b45131e6d54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:22,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4409ddcf-6d2b-4309-937d-4b45131e6d54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:22,939] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:22,939] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:39:22,939] [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
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.1101	59	686	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	75.9554	52	686	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	75.8879	51	686	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	75.8837	51	686	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	75.8605	52	686	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	75.6992	50	686	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	75.09	51	686	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:39:22,940] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23515/tc_result.tsv
[2023-03-19 01:39:22,941] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:22,942] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:22,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4409ddcf-6d2b-4309-937d-4b45131e6d54/dqc_reference/checkm_data
[2023-03-19 01:39:22,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:22,948] [INFO] Task started: CheckM
[2023-03-19 01:39:22,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23515/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23515/checkm_input OceanDNA-b23515/checkm_result
[2023-03-19 01:39:58,103] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:58,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:39:58,172] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:58,172] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:58,172] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23515/markers.fasta)
[2023-03-19 01:39:58,173] [INFO] Task started: Blastn
[2023-03-19 01:39:58,173] [INFO] Running command: blastn -query OceanDNA-b23515/markers.fasta -db /var/lib/cwl/stg4409ddcf-6d2b-4309-937d-4b45131e6d54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23515/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:59,245] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:59,267] [INFO] Selected 16 target genomes.
[2023-03-19 01:39:59,268] [INFO] Target genome list was writen to OceanDNA-b23515/target_genomes_gtdb.txt
[2023-03-19 01:39:59,295] [INFO] Task started: fastANI
[2023-03-19 01:39:59,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b1ac60-47fb-44e3-901b-de3c0698ff9f/OceanDNA-b23515.fa --refList OceanDNA-b23515/target_genomes_gtdb.txt --output OceanDNA-b23515/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:40:11,160] [INFO] Task succeeded: fastANI
[2023-03-19 01:40:11,165] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:40:11,166] [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_013213785.1	s__Henriciella sp013213785	85.718	581	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213825.1	s__Henriciella sp013213825	77.8178	237	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	77.4716	266	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642885.1	s__Henriciella sp017642885	77.3531	233	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCF_001854405.1	s__Henriciella sp001854405	77.2848	254	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222605.1	s__Hyphomonas sp002695785	75.6949	52	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCF_000682755.1	s__Hyphomonas beringensis	75.674	51	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:40:11,178] [INFO] GTDB search result was written to OceanDNA-b23515/result_gtdb.tsv
[2023-03-19 01:40:11,198] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:40:11,209] [INFO] DFAST_QC result json was written to OceanDNA-b23515/dqc_result.json
[2023-03-19 01:40:11,209] [INFO] DFAST_QC completed!
[2023-03-19 01:40:11,209] [INFO] Total running time: 0h1m17s