[2023-03-17 09:11:24,740] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:11:24,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:11:24,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg34a0b0df-08c8-4a54-a86e-6b3f6b4d4ad3/dqc_reference
[2023-03-17 09:11:26,038] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:11:26,039] [INFO] Task started: Prodigal
[2023-03-17 09:11:26,039] [INFO] Running command: cat /var/lib/cwl/stge41c9960-b009-40a7-b7e1-c39fdf96bc8e/OceanDNA-b31694.fa | prodigal -d OceanDNA-b31694/cds.fna -a OceanDNA-b31694/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:11:30,585] [INFO] Task succeeded: Prodigal
[2023-03-17 09:11:30,585] [INFO] Task started: HMMsearch
[2023-03-17 09:11:30,585] [INFO] Running command: hmmsearch --tblout OceanDNA-b31694/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34a0b0df-08c8-4a54-a86e-6b3f6b4d4ad3/dqc_reference/reference_markers.hmm OceanDNA-b31694/protein.faa > /dev/null
[2023-03-17 09:11:30,752] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:11:30,753] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge41c9960-b009-40a7-b7e1-c39fdf96bc8e/OceanDNA-b31694.fa]
[2023-03-17 09:11:30,764] [INFO] Query marker FASTA was written to OceanDNA-b31694/markers.fasta
[2023-03-17 09:11:30,765] [INFO] Task started: Blastn
[2023-03-17 09:11:30,765] [INFO] Running command: blastn -query OceanDNA-b31694/markers.fasta -db /var/lib/cwl/stg34a0b0df-08c8-4a54-a86e-6b3f6b4d4ad3/dqc_reference/reference_markers.fasta -out OceanDNA-b31694/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:11:31,771] [INFO] Task succeeded: Blastn
[2023-03-17 09:11:31,772] [INFO] Selected 25 target genomes.
[2023-03-17 09:11:31,772] [INFO] Target genome list was writen to OceanDNA-b31694/target_genomes.txt
[2023-03-17 09:11:31,837] [INFO] Task started: fastANI
[2023-03-17 09:11:31,837] [INFO] Running command: fastANI --query /var/lib/cwl/stge41c9960-b009-40a7-b7e1-c39fdf96bc8e/OceanDNA-b31694.fa --refList OceanDNA-b31694/target_genomes.txt --output OceanDNA-b31694/fastani_result.tsv --threads 1
[2023-03-17 09:11:43,474] [INFO] Task succeeded: fastANI
[2023-03-17 09:11:43,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34a0b0df-08c8-4a54-a86e-6b3f6b4d4ad3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:11:43,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34a0b0df-08c8-4a54-a86e-6b3f6b4d4ad3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:11:43,605] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:11:43,605] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:11:43,605] [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
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	80.1428	92	126	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.7703	86	126	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.6784	87	126	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.4445	89	126	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.3037	92	126	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	79.2878	79	126	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.2828	78	126	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.1671	85	126	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.0484	82	126	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	78.9525	67	126	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.9525	67	126	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	78.9216	72	126	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.9155	89	126	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.8646	66	126	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.8119	80	126	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.8119	88	126	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.774	81	126	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.7663	80	126	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	78.6926	77	126	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	78.6669	78	126	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	78.6611	81	126	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.6235	67	126	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.6041	64	126	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.4962	75	126	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.4182	64	126	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:11:43,605] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31694/tc_result.tsv
[2023-03-17 09:11:43,605] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:11:43,605] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:11:43,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34a0b0df-08c8-4a54-a86e-6b3f6b4d4ad3/dqc_reference/checkm_data
[2023-03-17 09:11:43,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:11:43,609] [INFO] Task started: CheckM
[2023-03-17 09:11:43,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31694/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31694/checkm_input OceanDNA-b31694/checkm_result
[2023-03-17 09:12:06,362] [INFO] Task succeeded: CheckM
[2023-03-17 09:12:06,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.83%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 09:12:06,364] [INFO] ===== Completeness check finished =====
[2023-03-17 09:12:06,365] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:12:06,365] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31694/markers.fasta)
[2023-03-17 09:12:06,366] [INFO] Task started: Blastn
[2023-03-17 09:12:06,366] [INFO] Running command: blastn -query OceanDNA-b31694/markers.fasta -db /var/lib/cwl/stg34a0b0df-08c8-4a54-a86e-6b3f6b4d4ad3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31694/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:12:08,217] [INFO] Task succeeded: Blastn
[2023-03-17 09:12:08,218] [INFO] Selected 18 target genomes.
[2023-03-17 09:12:08,218] [INFO] Target genome list was writen to OceanDNA-b31694/target_genomes_gtdb.txt
[2023-03-17 09:12:08,358] [INFO] Task started: fastANI
[2023-03-17 09:12:08,358] [INFO] Running command: fastANI --query /var/lib/cwl/stge41c9960-b009-40a7-b7e1-c39fdf96bc8e/OceanDNA-b31694.fa --refList OceanDNA-b31694/target_genomes_gtdb.txt --output OceanDNA-b31694/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:12:16,034] [INFO] Task succeeded: fastANI
[2023-03-17 09:12:16,044] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:12:16,045] [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_001678665.1	s__Qipengyuania sp001678665	88.5919	120	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	88.3529	114	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	86.5632	99	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_009827295.1	s__Qipengyuania pelagi	80.1428	92	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.6784	87	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	79.6634	90	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_014641655.1	s__Alteriqipengyuania_A marina	79.5839	82	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	-
GCF_011762005.1	s__Qipengyuania flava	79.3037	92	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_006542605.1	s__Erythrobacter sp006542605	79.2585	85	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	79.1671	85	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	79.0896	85	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.0484	82	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.8119	80	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	78.7155	82	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054555.1	s__Erythrobacter sp011054555	78.6933	71	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279825.1	s__Croceibacterium sp002279825	78.3034	73	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCF_014644315.1	s__Tsuneonella deserti	77.8063	62	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013370205.1	s__Actirhodobacter atriluteus	77.6224	63	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:12:16,045] [INFO] GTDB search result was written to OceanDNA-b31694/result_gtdb.tsv
[2023-03-17 09:12:16,045] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:12:16,047] [INFO] DFAST_QC result json was written to OceanDNA-b31694/dqc_result.json
[2023-03-17 09:12:16,047] [INFO] DFAST_QC completed!
[2023-03-17 09:12:16,047] [INFO] Total running time: 0h0m51s