[2023-03-19 01:21:54,512] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:21:54,512] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:21:54,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a219865-22fe-40a5-a8ff-a4d6ffef56df/dqc_reference
[2023-03-19 01:21:56,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:21:56,075] [INFO] Task started: Prodigal
[2023-03-19 01:21:56,075] [INFO] Running command: cat /var/lib/cwl/stgdbf0564b-7891-4070-bca9-a57dbb3da1e9/OceanDNA-b31581.fa | prodigal -d OceanDNA-b31581/cds.fna -a OceanDNA-b31581/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:22:13,640] [INFO] Task succeeded: Prodigal
[2023-03-19 01:22:13,640] [INFO] Task started: HMMsearch
[2023-03-19 01:22:13,640] [INFO] Running command: hmmsearch --tblout OceanDNA-b31581/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a219865-22fe-40a5-a8ff-a4d6ffef56df/dqc_reference/reference_markers.hmm OceanDNA-b31581/protein.faa > /dev/null
[2023-03-19 01:22:13,800] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:22:13,801] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdbf0564b-7891-4070-bca9-a57dbb3da1e9/OceanDNA-b31581.fa]
[2023-03-19 01:22:13,818] [INFO] Query marker FASTA was written to OceanDNA-b31581/markers.fasta
[2023-03-19 01:22:13,820] [INFO] Task started: Blastn
[2023-03-19 01:22:13,820] [INFO] Running command: blastn -query OceanDNA-b31581/markers.fasta -db /var/lib/cwl/stg6a219865-22fe-40a5-a8ff-a4d6ffef56df/dqc_reference/reference_markers.fasta -out OceanDNA-b31581/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:22:14,490] [INFO] Task succeeded: Blastn
[2023-03-19 01:22:14,491] [INFO] Selected 16 target genomes.
[2023-03-19 01:22:14,491] [INFO] Target genome list was writen to OceanDNA-b31581/target_genomes.txt
[2023-03-19 01:22:14,502] [INFO] Task started: fastANI
[2023-03-19 01:22:14,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbf0564b-7891-4070-bca9-a57dbb3da1e9/OceanDNA-b31581.fa --refList OceanDNA-b31581/target_genomes.txt --output OceanDNA-b31581/fastani_result.tsv --threads 1
[2023-03-19 01:22:23,904] [INFO] Task succeeded: fastANI
[2023-03-19 01:22:23,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a219865-22fe-40a5-a8ff-a4d6ffef56df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:22:23,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a219865-22fe-40a5-a8ff-a4d6ffef56df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:22:23,915] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:22:23,915] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:22:23,915] [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
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	85.6216	663	933	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	83.7141	647	933	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	83.6588	659	933	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.0766	421	933	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.8934	368	933	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.8412	375	933	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.7211	419	933	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.6593	390	933	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.6495	363	933	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.5719	372	933	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.5433	386	933	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.5201	360	933	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.2713	325	933	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.2045	327	933	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.0931	266	933	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.6423	249	933	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:22:23,915] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31581/tc_result.tsv
[2023-03-19 01:22:23,915] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:22:23,915] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:22:23,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a219865-22fe-40a5-a8ff-a4d6ffef56df/dqc_reference/checkm_data
[2023-03-19 01:22:23,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:22:23,920] [INFO] Task started: CheckM
[2023-03-19 01:22:23,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31581/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31581/checkm_input OceanDNA-b31581/checkm_result
[2023-03-19 01:23:08,013] [INFO] Task succeeded: CheckM
[2023-03-19 01:23:08,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:23:08,015] [INFO] ===== Completeness check finished =====
[2023-03-19 01:23:08,016] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:23:08,016] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31581/markers.fasta)
[2023-03-19 01:23:08,017] [INFO] Task started: Blastn
[2023-03-19 01:23:08,017] [INFO] Running command: blastn -query OceanDNA-b31581/markers.fasta -db /var/lib/cwl/stg6a219865-22fe-40a5-a8ff-a4d6ffef56df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31581/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:23:09,196] [INFO] Task succeeded: Blastn
[2023-03-19 01:23:09,196] [INFO] Selected 7 target genomes.
[2023-03-19 01:23:09,196] [INFO] Target genome list was writen to OceanDNA-b31581/target_genomes_gtdb.txt
[2023-03-19 01:23:09,205] [INFO] Task started: fastANI
[2023-03-19 01:23:09,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbf0564b-7891-4070-bca9-a57dbb3da1e9/OceanDNA-b31581.fa --refList OceanDNA-b31581/target_genomes_gtdb.txt --output OceanDNA-b31581/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:23:13,764] [INFO] Task succeeded: fastANI
[2023-03-19 01:23:13,769] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:23:13,769] [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_002729695.1	s__Alteriqipengyuania sp002729695	88.3334	697	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	85.4055	666	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	85.3696	686	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	83.9089	642	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCF_003363135.1	s__Alteriqipengyuania lutimaris	83.645	660	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	83.6184	616	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	83.388	343	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:23:13,769] [INFO] GTDB search result was written to OceanDNA-b31581/result_gtdb.tsv
[2023-03-19 01:23:13,770] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:23:13,771] [INFO] DFAST_QC result json was written to OceanDNA-b31581/dqc_result.json
[2023-03-19 01:23:13,771] [INFO] DFAST_QC completed!
[2023-03-19 01:23:13,771] [INFO] Total running time: 0h1m19s