[2023-03-14 12:28:23,284] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:28:23,285] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:28:23,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg497d192a-803a-4ec1-bc40-0f01a383d871/dqc_reference
[2023-03-14 12:28:25,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:28:25,336] [INFO] Task started: Prodigal
[2023-03-14 12:28:25,337] [INFO] Running command: cat /var/lib/cwl/stg1b48fa8b-125c-4c3f-8f64-835cc3df0445/OceanDNA-b31947.fa | prodigal -d OceanDNA-b31947/cds.fna -a OceanDNA-b31947/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:28:44,514] [INFO] Task succeeded: Prodigal
[2023-03-14 12:28:44,515] [INFO] Task started: HMMsearch
[2023-03-14 12:28:44,515] [INFO] Running command: hmmsearch --tblout OceanDNA-b31947/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg497d192a-803a-4ec1-bc40-0f01a383d871/dqc_reference/reference_markers.hmm OceanDNA-b31947/protein.faa > /dev/null
[2023-03-14 12:28:44,704] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:28:44,705] [INFO] Found 6/6 markers.
[2023-03-14 12:28:44,723] [INFO] Query marker FASTA was written to OceanDNA-b31947/markers.fasta
[2023-03-14 12:28:44,724] [INFO] Task started: Blastn
[2023-03-14 12:28:44,724] [INFO] Running command: blastn -query OceanDNA-b31947/markers.fasta -db /var/lib/cwl/stg497d192a-803a-4ec1-bc40-0f01a383d871/dqc_reference/reference_markers.fasta -out OceanDNA-b31947/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:28:45,566] [INFO] Task succeeded: Blastn
[2023-03-14 12:28:45,567] [INFO] Selected 14 target genomes.
[2023-03-14 12:28:45,567] [INFO] Target genome list was writen to OceanDNA-b31947/target_genomes.txt
[2023-03-14 12:28:45,579] [INFO] Task started: fastANI
[2023-03-14 12:28:45,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b48fa8b-125c-4c3f-8f64-835cc3df0445/OceanDNA-b31947.fa --refList OceanDNA-b31947/target_genomes.txt --output OceanDNA-b31947/fastani_result.tsv --threads 1
[2023-03-14 12:28:54,716] [INFO] Task succeeded: fastANI
[2023-03-14 12:28:54,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg497d192a-803a-4ec1-bc40-0f01a383d871/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:28:54,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg497d192a-803a-4ec1-bc40-0f01a383d871/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:28:54,726] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 12:28:54,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 12:28:54,726] [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
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	99.5375	936	955	95	conclusive
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	84.4614	710	955	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	81.4454	616	955	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	79.8185	524	955	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	79.7252	520	955	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	79.7167	515	955	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.9879	401	955	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.6454	362	955	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.6217	331	955	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.6144	351	955	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.5265	341	955	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	78.4706	420	955	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.3418	316	955	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.032	271	955	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:28:54,726] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31947/tc_result.tsv
[2023-03-14 12:28:54,726] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:28:54,726] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:28:54,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg497d192a-803a-4ec1-bc40-0f01a383d871/dqc_reference/checkm_data
[2023-03-14 12:28:54,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:28:54,732] [INFO] Task started: CheckM
[2023-03-14 12:28:54,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31947/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31947/checkm_input OceanDNA-b31947/checkm_result
[2023-03-14 12:29:42,471] [INFO] Task succeeded: CheckM
[2023-03-14 12:29:42,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:29:42,474] [INFO] ===== Completeness check finished =====
[2023-03-14 12:29:42,474] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:29:42,474] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31947/markers.fasta)
[2023-03-14 12:29:42,475] [INFO] Task started: Blastn
[2023-03-14 12:29:42,475] [INFO] Running command: blastn -query OceanDNA-b31947/markers.fasta -db /var/lib/cwl/stg497d192a-803a-4ec1-bc40-0f01a383d871/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31947/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:29:44,263] [INFO] Task succeeded: Blastn
[2023-03-14 12:29:44,265] [INFO] Selected 12 target genomes.
[2023-03-14 12:29:44,265] [INFO] Target genome list was writen to OceanDNA-b31947/target_genomes_gtdb.txt
[2023-03-14 12:29:44,276] [INFO] Task started: fastANI
[2023-03-14 12:29:44,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b48fa8b-125c-4c3f-8f64-835cc3df0445/OceanDNA-b31947.fa --refList OceanDNA-b31947/target_genomes_gtdb.txt --output OceanDNA-b31947/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:29:52,346] [INFO] Task succeeded: fastANI
[2023-03-14 12:29:52,353] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:29:52,354] [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
GCF_003584125.1	s__Alteraurantiacibacter zhengii	99.5375	936	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003605195.1	s__Alteraurantiacibacter odishensis	84.465	710	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	81.4341	617	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	79.8185	524	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	79.717	515	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	79.6035	459	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	79.2137	406	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584015.1	s__Alteraurantiacibacter xanthus	79.2041	428	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	79.1686	422	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	79.1352	451	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	79.0986	472	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	78.0804	334	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:29:52,354] [INFO] GTDB search result was written to OceanDNA-b31947/result_gtdb.tsv
[2023-03-14 12:29:52,354] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:29:52,356] [INFO] DFAST_QC result json was written to OceanDNA-b31947/dqc_result.json
[2023-03-14 12:29:52,356] [INFO] DFAST_QC completed!
[2023-03-14 12:29:52,356] [INFO] Total running time: 0h1m29s