[2023-03-15 22:23:01,937] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:23:01,937] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:23:01,938] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9eebb46-3e35-4a32-80c8-72b131272bc8/dqc_reference
[2023-03-15 22:23:03,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:23:03,673] [INFO] Task started: Prodigal
[2023-03-15 22:23:03,673] [INFO] Running command: cat /var/lib/cwl/stgbafea11a-7496-4243-ba0e-ab3b22981892/OceanDNA-b31557.fa | prodigal -d OceanDNA-b31557/cds.fna -a OceanDNA-b31557/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:23:11,718] [INFO] Task succeeded: Prodigal
[2023-03-15 22:23:11,719] [INFO] Task started: HMMsearch
[2023-03-15 22:23:11,719] [INFO] Running command: hmmsearch --tblout OceanDNA-b31557/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9eebb46-3e35-4a32-80c8-72b131272bc8/dqc_reference/reference_markers.hmm OceanDNA-b31557/protein.faa > /dev/null
[2023-03-15 22:23:11,872] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:23:11,872] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbafea11a-7496-4243-ba0e-ab3b22981892/OceanDNA-b31557.fa]
[2023-03-15 22:23:11,885] [INFO] Query marker FASTA was written to OceanDNA-b31557/markers.fasta
[2023-03-15 22:23:11,886] [INFO] Task started: Blastn
[2023-03-15 22:23:11,887] [INFO] Running command: blastn -query OceanDNA-b31557/markers.fasta -db /var/lib/cwl/stgd9eebb46-3e35-4a32-80c8-72b131272bc8/dqc_reference/reference_markers.fasta -out OceanDNA-b31557/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:12,512] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:12,513] [INFO] Selected 25 target genomes.
[2023-03-15 22:23:12,514] [INFO] Target genome list was writen to OceanDNA-b31557/target_genomes.txt
[2023-03-15 22:23:12,529] [INFO] Task started: fastANI
[2023-03-15 22:23:12,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgbafea11a-7496-4243-ba0e-ab3b22981892/OceanDNA-b31557.fa --refList OceanDNA-b31557/target_genomes.txt --output OceanDNA-b31557/fastani_result.tsv --threads 1
[2023-03-15 22:23:23,687] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:23,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9eebb46-3e35-4a32-80c8-72b131272bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:23:23,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9eebb46-3e35-4a32-80c8-72b131272bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:23:23,701] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 22:23:23,701] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 22:23:23,701] [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
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	98.1659	381	387	95	conclusive
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	98.1353	382	387	95	conclusive
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.1142	90	387	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.0019	83	387	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	76.9044	75	387	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	76.8389	62	387	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	76.7901	71	387	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	76.7883	75	387	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	76.7278	88	387	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	76.7054	70	387	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	76.6848	81	387	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	76.6824	127	387	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	76.6682	82	387	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	76.6656	78	387	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	76.6431	70	387	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	76.6431	70	387	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	76.6422	84	387	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	76.5284	77	387	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	76.5	51	387	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	76.387	79	387	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.3695	65	387	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	76.1163	82	387	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	76.1163	82	387	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	75.9312	60	387	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:23:23,701] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31557/tc_result.tsv
[2023-03-15 22:23:23,701] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:23:23,701] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:23:23,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9eebb46-3e35-4a32-80c8-72b131272bc8/dqc_reference/checkm_data
[2023-03-15 22:23:23,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:23:23,745] [INFO] Task started: CheckM
[2023-03-15 22:23:23,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31557/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31557/checkm_input OceanDNA-b31557/checkm_result
[2023-03-15 22:23:48,549] [INFO] Task succeeded: CheckM
[2023-03-15 22:23:48,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 34.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:23:48,551] [INFO] ===== Completeness check finished =====
[2023-03-15 22:23:48,552] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:23:48,552] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31557/markers.fasta)
[2023-03-15 22:23:48,553] [INFO] Task started: Blastn
[2023-03-15 22:23:48,553] [INFO] Running command: blastn -query OceanDNA-b31557/markers.fasta -db /var/lib/cwl/stgd9eebb46-3e35-4a32-80c8-72b131272bc8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31557/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:49,514] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:49,515] [INFO] Selected 19 target genomes.
[2023-03-15 22:23:49,515] [INFO] Target genome list was writen to OceanDNA-b31557/target_genomes_gtdb.txt
[2023-03-15 22:23:49,536] [INFO] Task started: fastANI
[2023-03-15 22:23:49,536] [INFO] Running command: fastANI --query /var/lib/cwl/stgbafea11a-7496-4243-ba0e-ab3b22981892/OceanDNA-b31557.fa --refList OceanDNA-b31557/target_genomes_gtdb.txt --output OceanDNA-b31557/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:23:58,251] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:58,261] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:23:58,261] [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_001663155.1	s__Erythrobacter ishigakiensis	98.1659	381	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	97.03	96.25	0.95	0.94	6	conclusive
GCA_003149575.1	s__Erythrobacter sp003149575	79.8849	241	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	98.16	98.16	0.93	0.93	2	-
GCA_013002295.1	s__Erythrobacter sp013002295	79.7984	201	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.14	98.90	0.85	0.82	4	-
GCF_011047315.1	s__Erythrobacter sp011047315	77.5675	176	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	77.3256	105	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	77.3205	122	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001515985.1	s__Erythrobacter sp001515985	77.1961	117	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014983025.1	s__Erythrobacter sp014983025	77.1247	86	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	76.7578	65	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705715.1	s__Erythrobacter sp014705715	76.7047	89	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371495.1	s__Erythrobacter sp013371495	76.6824	127	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	76.5228	66	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152865.1	s__Erythrobacter sp000152865	76.4965	104	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542875.1	s__Erythrobacter sp001542875	76.4316	77	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720465.1	s__Erythrobacter sp001720465	76.251	92	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001296025.1	s__Erythrobacter sp001296025	76.2346	80	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013260645.1	s__Qipengyuania mangrovi	76.1534	72	387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:23:58,261] [INFO] GTDB search result was written to OceanDNA-b31557/result_gtdb.tsv
[2023-03-15 22:23:58,261] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:23:58,263] [INFO] DFAST_QC result json was written to OceanDNA-b31557/dqc_result.json
[2023-03-15 22:23:58,263] [INFO] DFAST_QC completed!
[2023-03-15 22:23:58,263] [INFO] Total running time: 0h0m56s