[2023-03-16 04:20:43,481] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:20:43,481] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:20:43,481] [INFO] DQC Reference Directory: /var/lib/cwl/stgb768c02c-5e2b-4048-a803-aeb17d045660/dqc_reference
[2023-03-16 04:20:44,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:20:44,609] [INFO] Task started: Prodigal
[2023-03-16 04:20:44,609] [INFO] Running command: cat /var/lib/cwl/stga2d9620a-cc06-471f-9fb0-c23beffd92b7/OceanDNA-b31945.fa | prodigal -d OceanDNA-b31945/cds.fna -a OceanDNA-b31945/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:20:55,728] [INFO] Task succeeded: Prodigal
[2023-03-16 04:20:55,728] [INFO] Task started: HMMsearch
[2023-03-16 04:20:55,728] [INFO] Running command: hmmsearch --tblout OceanDNA-b31945/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb768c02c-5e2b-4048-a803-aeb17d045660/dqc_reference/reference_markers.hmm OceanDNA-b31945/protein.faa > /dev/null
[2023-03-16 04:20:55,892] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:20:55,893] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga2d9620a-cc06-471f-9fb0-c23beffd92b7/OceanDNA-b31945.fa]
[2023-03-16 04:20:55,909] [INFO] Query marker FASTA was written to OceanDNA-b31945/markers.fasta
[2023-03-16 04:20:55,910] [INFO] Task started: Blastn
[2023-03-16 04:20:55,910] [INFO] Running command: blastn -query OceanDNA-b31945/markers.fasta -db /var/lib/cwl/stgb768c02c-5e2b-4048-a803-aeb17d045660/dqc_reference/reference_markers.fasta -out OceanDNA-b31945/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:20:56,610] [INFO] Task succeeded: Blastn
[2023-03-16 04:20:56,611] [INFO] Selected 16 target genomes.
[2023-03-16 04:20:56,611] [INFO] Target genome list was writen to OceanDNA-b31945/target_genomes.txt
[2023-03-16 04:20:56,619] [INFO] Task started: fastANI
[2023-03-16 04:20:56,619] [INFO] Running command: fastANI --query /var/lib/cwl/stga2d9620a-cc06-471f-9fb0-c23beffd92b7/OceanDNA-b31945.fa --refList OceanDNA-b31945/target_genomes.txt --output OceanDNA-b31945/fastani_result.tsv --threads 1
[2023-03-16 04:21:04,407] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:04,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb768c02c-5e2b-4048-a803-aeb17d045660/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:21:04,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb768c02c-5e2b-4048-a803-aeb17d045660/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:21:04,417] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:21:04,417] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:21:04,417] [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 rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	82.5402	430	556	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	80.5419	395	556	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	80.303	371	556	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	78.7507	282	556	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	78.7316	285	556	95	below_threshold
Aurantiacibacter arachoides	strain=RC4-10-4	GCA_009827335.1	1850444	1850444	type	True	78.1859	259	556	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	78.1419	256	556	95	below_threshold
Aurantiacibacter marinus	strain=KCTC 23554	GCA_001021555.1	874156	874156	type	True	78.067	209	556	95	below_threshold
Aurantiacibacter marinus	strain=HWDM-33	GCA_001013305.1	874156	874156	type	True	77.9788	215	556	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	77.8608	212	556	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	77.7352	195	556	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.3177	160	556	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.2701	156	556	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	77.2554	150	556	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.2188	147	556	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.1923	138	556	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:21:04,417] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31945/tc_result.tsv
[2023-03-16 04:21:04,417] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:21:04,417] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:21:04,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb768c02c-5e2b-4048-a803-aeb17d045660/dqc_reference/checkm_data
[2023-03-16 04:21:04,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:21:04,422] [INFO] Task started: CheckM
[2023-03-16 04:21:04,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31945/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31945/checkm_input OceanDNA-b31945/checkm_result
[2023-03-16 04:21:36,015] [INFO] Task succeeded: CheckM
[2023-03-16 04:21:36,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.96%
Contamintation: 2.43%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 04:21:36,018] [INFO] ===== Completeness check finished =====
[2023-03-16 04:21:36,018] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:21:36,018] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31945/markers.fasta)
[2023-03-16 04:21:36,018] [INFO] Task started: Blastn
[2023-03-16 04:21:36,018] [INFO] Running command: blastn -query OceanDNA-b31945/markers.fasta -db /var/lib/cwl/stgb768c02c-5e2b-4048-a803-aeb17d045660/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31945/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:21:37,209] [INFO] Task succeeded: Blastn
[2023-03-16 04:21:37,209] [INFO] Selected 16 target genomes.
[2023-03-16 04:21:37,209] [INFO] Target genome list was writen to OceanDNA-b31945/target_genomes_gtdb.txt
[2023-03-16 04:21:37,227] [INFO] Task started: fastANI
[2023-03-16 04:21:37,227] [INFO] Running command: fastANI --query /var/lib/cwl/stga2d9620a-cc06-471f-9fb0-c23beffd92b7/OceanDNA-b31945.fa --refList OceanDNA-b31945/target_genomes_gtdb.txt --output OceanDNA-b31945/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:21:45,555] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:45,565] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:21:45,565] [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_009807005.1	s__Alteraurantiacibacter rhizosphaerae	82.5462	430	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	80.5266	396	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	80.2871	372	556	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	78.7663	281	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	78.124	235	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021555.1	s__Alteraurantiacibacter marinus	78.067	209	556	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	78.0201	248	556	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	77.9331	200	556	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	77.8855	209	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019885.1	s__Alteraurantiacibacter sp016019885	77.8608	212	556	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	77.8045	238	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	77.7999	171	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	77.7352	195	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584015.1	s__Alteraurantiacibacter xanthus	77.6134	217	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367375.1	s__Alteraurantiacibacter sp002367375	77.6071	212	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827305.1	s__Croceibacterium xixiisoli	77.2396	151	556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:21:45,565] [INFO] GTDB search result was written to OceanDNA-b31945/result_gtdb.tsv
[2023-03-16 04:21:45,565] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:21:45,567] [INFO] DFAST_QC result json was written to OceanDNA-b31945/dqc_result.json
[2023-03-16 04:21:45,567] [INFO] DFAST_QC completed!
[2023-03-16 04:21:45,567] [INFO] Total running time: 0h1m2s