[2024-01-25 18:00:20,930] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:20,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:20,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f2eb88a-b816-4370-80a1-d90c12a03bbc/dqc_reference
[2024-01-25 18:00:22,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:22,085] [INFO] Task started: Prodigal
[2024-01-25 18:00:22,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg38410031-3de2-4f19-ad7a-94615ece59df/GCF_009828025.1_ASM982802v1_genomic.fna.gz | prodigal -d GCF_009828025.1_ASM982802v1_genomic.fna/cds.fna -a GCF_009828025.1_ASM982802v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:30,932] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:30,933] [INFO] Task started: HMMsearch
[2024-01-25 18:00:30,933] [INFO] Running command: hmmsearch --tblout GCF_009828025.1_ASM982802v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f2eb88a-b816-4370-80a1-d90c12a03bbc/dqc_reference/reference_markers.hmm GCF_009828025.1_ASM982802v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:31,132] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:31,133] [INFO] Found 6/6 markers.
[2024-01-25 18:00:31,159] [INFO] Query marker FASTA was written to GCF_009828025.1_ASM982802v1_genomic.fna/markers.fasta
[2024-01-25 18:00:31,159] [INFO] Task started: Blastn
[2024-01-25 18:00:31,160] [INFO] Running command: blastn -query GCF_009828025.1_ASM982802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f2eb88a-b816-4370-80a1-d90c12a03bbc/dqc_reference/reference_markers.fasta -out GCF_009828025.1_ASM982802v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:31,971] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:31,974] [INFO] Selected 22 target genomes.
[2024-01-25 18:00:31,974] [INFO] Target genome list was writen to GCF_009828025.1_ASM982802v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:32,008] [INFO] Task started: fastANI
[2024-01-25 18:00:32,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg38410031-3de2-4f19-ad7a-94615ece59df/GCF_009828025.1_ASM982802v1_genomic.fna.gz --refList GCF_009828025.1_ASM982802v1_genomic.fna/target_genomes.txt --output GCF_009828025.1_ASM982802v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:00:44,310] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:44,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f2eb88a-b816-4370-80a1-d90c12a03bbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:00:44,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f2eb88a-b816-4370-80a1-d90c12a03bbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:00:44,323] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:00:44,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:00:44,323] [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 algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	100.0	1059	1061	95	conclusive
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.5357	424	1061	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.3135	442	1061	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.2087	396	1061	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.1868	378	1061	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.0725	364	1061	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.0128	377	1061	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.0095	399	1061	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	78.999	374	1061	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.9852	344	1061	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.9358	372	1061	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.9186	404	1061	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	78.843	362	1061	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.7753	346	1061	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.6859	350	1061	95	below_threshold
Tsuneonella suprasediminis	strain=Ery12	GCA_003605755.1	2306996	2306996	type	True	78.3413	300	1061	95	below_threshold
Tsuneonella aeria	strain=100921-2	GCA_009827495.1	1837929	1837929	type	True	78.3166	280	1061	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.2063	267	1061	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.1769	251	1061	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.1432	277	1061	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	77.9219	252	1061	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	77.4959	218	1061	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:00:44,324] [INFO] DFAST Taxonomy check result was written to GCF_009828025.1_ASM982802v1_genomic.fna/tc_result.tsv
[2024-01-25 18:00:44,325] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:00:44,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:00:44,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f2eb88a-b816-4370-80a1-d90c12a03bbc/dqc_reference/checkm_data
[2024-01-25 18:00:44,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:00:44,359] [INFO] Task started: CheckM
[2024-01-25 18:00:44,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828025.1_ASM982802v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828025.1_ASM982802v1_genomic.fna/checkm_input GCF_009828025.1_ASM982802v1_genomic.fna/checkm_result
[2024-01-25 18:01:12,904] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:12,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:12,926] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:12,926] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:12,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828025.1_ASM982802v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:12,926] [INFO] Task started: Blastn
[2024-01-25 18:01:12,927] [INFO] Running command: blastn -query GCF_009828025.1_ASM982802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f2eb88a-b816-4370-80a1-d90c12a03bbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828025.1_ASM982802v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:14,479] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:14,482] [INFO] Selected 25 target genomes.
[2024-01-25 18:01:14,482] [INFO] Target genome list was writen to GCF_009828025.1_ASM982802v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:14,508] [INFO] Task started: fastANI
[2024-01-25 18:01:14,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg38410031-3de2-4f19-ad7a-94615ece59df/GCF_009828025.1_ASM982802v1_genomic.fna.gz --refList GCF_009828025.1_ASM982802v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828025.1_ASM982802v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:30,229] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:30,244] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:30,244] [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_009828025.1	s__Qipengyuania algicida	100.0	1059	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018828205.1	s__Qipengyuania sp018828205	79.3745	352	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	79.3028	443	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	79.219	325	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.1915	398	1061	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	79.1736	368	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001678665.1	s__Qipengyuania sp001678665	79.1371	409	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	79.0943	417	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCA_009993605.1	s__Qipengyuania sp009993605	79.0933	419	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013260645.1	s__Qipengyuania mangrovi	79.0659	380	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355455.1	s__Qipengyuania aurea	79.058	387	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_004114695.1	s__Parerythrobacter sp004114695	79.0563	369	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000181515.1	s__Qipengyuania sp000181515	79.0279	402	1061	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	78.9951	355	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.9562	363	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.9524	372	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.9285	403	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	78.8671	336	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	78.7156	312	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005884405.1	s__Qipengyuania marisflavi	78.577	366	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	78.5535	315	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	78.3885	270	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCA_017302615.1	s__Novosphingobium sp017302615	78.2599	292	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320115.1	s__Croceibacterium segetis	78.2123	273	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.1011	276	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:30,246] [INFO] GTDB search result was written to GCF_009828025.1_ASM982802v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:30,246] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:30,250] [INFO] DFAST_QC result json was written to GCF_009828025.1_ASM982802v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:30,250] [INFO] DFAST_QC completed!
[2024-01-25 18:01:30,250] [INFO] Total running time: 0h1m9s