[2023-03-18 08:36:16,002] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,002] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,002] [INFO] DQC Reference Directory: /var/lib/cwl/stg796fbec4-9806-4b59-b7a1-8f9e18d7c03e/dqc_reference
[2023-03-18 08:36:17,823] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,823] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,824] [INFO] Running command: cat /var/lib/cwl/stg9862a190-0d74-48c0-8a87-79e6f2dc79c3/OceanDNA-b31968.fa | prodigal -d OceanDNA-b31968/cds.fna -a OceanDNA-b31968/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:35,991] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:35,992] [INFO] Task started: HMMsearch
[2023-03-18 08:36:35,992] [INFO] Running command: hmmsearch --tblout OceanDNA-b31968/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg796fbec4-9806-4b59-b7a1-8f9e18d7c03e/dqc_reference/reference_markers.hmm OceanDNA-b31968/protein.faa > /dev/null
[2023-03-18 08:36:36,202] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:36,203] [INFO] Found 6/6 markers.
[2023-03-18 08:36:36,223] [INFO] Query marker FASTA was written to OceanDNA-b31968/markers.fasta
[2023-03-18 08:36:36,224] [INFO] Task started: Blastn
[2023-03-18 08:36:36,224] [INFO] Running command: blastn -query OceanDNA-b31968/markers.fasta -db /var/lib/cwl/stg796fbec4-9806-4b59-b7a1-8f9e18d7c03e/dqc_reference/reference_markers.fasta -out OceanDNA-b31968/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:36,986] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:36,987] [INFO] Selected 30 target genomes.
[2023-03-18 08:36:36,987] [INFO] Target genome list was writen to OceanDNA-b31968/target_genomes.txt
[2023-03-18 08:36:37,022] [INFO] Task started: fastANI
[2023-03-18 08:36:37,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg9862a190-0d74-48c0-8a87-79e6f2dc79c3/OceanDNA-b31968.fa --refList OceanDNA-b31968/target_genomes.txt --output OceanDNA-b31968/fastani_result.tsv --threads 1
[2023-03-18 08:36:54,742] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:54,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg796fbec4-9806-4b59-b7a1-8f9e18d7c03e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:54,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg796fbec4-9806-4b59-b7a1-8f9e18d7c03e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:54,758] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:54,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:36:54,758] [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
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	80.9795	376	960	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	80.137	451	960	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.4917	356	960	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.4003	373	960	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	79.1862	382	960	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.1801	296	960	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.1364	345	960	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.0665	343	960	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	79.0446	383	960	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.8269	280	960	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.8162	375	960	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.8112	326	960	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.808	265	960	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.8051	320	960	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.792	288	960	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.785	320	960	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.7456	308	960	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.7279	282	960	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	78.7179	319	960	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.6978	315	960	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	78.6364	333	960	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	78.4969	282	960	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.4464	313	960	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.4447	299	960	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	78.3701	333	960	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.33	333	960	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	78.2313	309	960	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	78.0978	287	960	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	77.7996	254	960	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	77.7662	269	960	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:36:54,759] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31968/tc_result.tsv
[2023-03-18 08:36:54,759] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:54,759] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:54,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg796fbec4-9806-4b59-b7a1-8f9e18d7c03e/dqc_reference/checkm_data
[2023-03-18 08:36:54,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:54,765] [INFO] Task started: CheckM
[2023-03-18 08:36:54,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31968/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31968/checkm_input OceanDNA-b31968/checkm_result
[2023-03-18 08:37:40,647] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:40,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:40,670] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:40,670] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:40,670] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31968/markers.fasta)
[2023-03-18 08:37:40,671] [INFO] Task started: Blastn
[2023-03-18 08:37:40,671] [INFO] Running command: blastn -query OceanDNA-b31968/markers.fasta -db /var/lib/cwl/stg796fbec4-9806-4b59-b7a1-8f9e18d7c03e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31968/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:41,947] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:41,949] [INFO] Selected 23 target genomes.
[2023-03-18 08:37:41,949] [INFO] Target genome list was writen to OceanDNA-b31968/target_genomes_gtdb.txt
[2023-03-18 08:37:41,965] [INFO] Task started: fastANI
[2023-03-18 08:37:41,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg9862a190-0d74-48c0-8a87-79e6f2dc79c3/OceanDNA-b31968.fa --refList OceanDNA-b31968/target_genomes_gtdb.txt --output OceanDNA-b31968/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:55,946] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:55,959] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:37:55,959] [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_002341345.1	s__Alteraurantiacibacter sp002341345	99.6361	756	960	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_003584015.1	s__Alteraurantiacibacter xanthus	80.1466	451	960	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	79.9246	381	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	79.6158	442	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.532	353	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	79.3135	359	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	79.2355	361	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	79.1738	383	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	79.1364	345	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.1221	354	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_014359685.1	s__Croceibacterium sp014359685	79.0977	257	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.0339	359	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	78.8512	348	960	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	78.8017	357	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698205.1	s__Tsuneonella dongtanensis	78.7723	283	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.7279	282	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958625.1	s__Tsuneonella rigui	78.4823	283	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	78.41	301	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143235.1	s__Erythrobacter sanguineus	78.3988	331	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001683845.1	s__Croceibacterium sp001683845	78.3651	303	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320115.1	s__Croceibacterium segetis	78.3484	318	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	78.2825	214	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_003660445.1	s__Croceibacterium ferulae	78.2191	310	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:55,962] [INFO] GTDB search result was written to OceanDNA-b31968/result_gtdb.tsv
[2023-03-18 08:37:55,963] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:55,967] [INFO] DFAST_QC result json was written to OceanDNA-b31968/dqc_result.json
[2023-03-18 08:37:55,967] [INFO] DFAST_QC completed!
[2023-03-18 08:37:55,967] [INFO] Total running time: 0h1m40s