[2024-01-24 12:23:35,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e6cf91e-5c3c-404d-9fcc-def8780f1cda/dqc_reference
[2024-01-24 12:23:36,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:36,293] [INFO] Task started: Prodigal
[2024-01-24 12:23:36,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg17420e2e-ea74-4b74-9ebd-47597953fb53/GCF_004965515.1_ASM496551v1_genomic.fna.gz | prodigal -d GCF_004965515.1_ASM496551v1_genomic.fna/cds.fna -a GCF_004965515.1_ASM496551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:47,568] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:47,568] [INFO] Task started: HMMsearch
[2024-01-24 12:23:47,568] [INFO] Running command: hmmsearch --tblout GCF_004965515.1_ASM496551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e6cf91e-5c3c-404d-9fcc-def8780f1cda/dqc_reference/reference_markers.hmm GCF_004965515.1_ASM496551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:47,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:47,773] [INFO] Found 6/6 markers.
[2024-01-24 12:23:47,805] [INFO] Query marker FASTA was written to GCF_004965515.1_ASM496551v1_genomic.fna/markers.fasta
[2024-01-24 12:23:47,805] [INFO] Task started: Blastn
[2024-01-24 12:23:47,805] [INFO] Running command: blastn -query GCF_004965515.1_ASM496551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e6cf91e-5c3c-404d-9fcc-def8780f1cda/dqc_reference/reference_markers.fasta -out GCF_004965515.1_ASM496551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:48,702] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:48,705] [INFO] Selected 25 target genomes.
[2024-01-24 12:23:48,706] [INFO] Target genome list was writen to GCF_004965515.1_ASM496551v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:48,713] [INFO] Task started: fastANI
[2024-01-24 12:23:48,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg17420e2e-ea74-4b74-9ebd-47597953fb53/GCF_004965515.1_ASM496551v1_genomic.fna.gz --refList GCF_004965515.1_ASM496551v1_genomic.fna/target_genomes.txt --output GCF_004965515.1_ASM496551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:02,731] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:02,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e6cf91e-5c3c-404d-9fcc-def8780f1cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:02,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e6cf91e-5c3c-404d-9fcc-def8780f1cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:02,750] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:02,750] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:02,751] [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
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	81.0626	499	1143	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.9953	540	1143	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	79.7381	500	1143	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	79.7068	485	1143	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	79.6458	456	1143	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	79.539	465	1143	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	79.498	515	1143	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.4846	408	1143	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	79.3179	509	1143	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.3016	392	1143	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	79.2794	486	1143	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	79.2327	487	1143	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.1869	387	1143	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	79.0823	398	1143	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.0792	424	1143	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.0508	371	1143	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.918	335	1143	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	78.868	405	1143	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.8485	336	1143	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	78.8226	383	1143	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.8204	381	1143	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.8097	383	1143	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.64	364	1143	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	78.541	379	1143	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.5305	381	1143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:02,753] [INFO] DFAST Taxonomy check result was written to GCF_004965515.1_ASM496551v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:02,753] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:02,753] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:02,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e6cf91e-5c3c-404d-9fcc-def8780f1cda/dqc_reference/checkm_data
[2024-01-24 12:24:02,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:02,788] [INFO] Task started: CheckM
[2024-01-24 12:24:02,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004965515.1_ASM496551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004965515.1_ASM496551v1_genomic.fna/checkm_input GCF_004965515.1_ASM496551v1_genomic.fna/checkm_result
[2024-01-24 12:24:35,758] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:35,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:35,780] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:35,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:35,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004965515.1_ASM496551v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:35,781] [INFO] Task started: Blastn
[2024-01-24 12:24:35,781] [INFO] Running command: blastn -query GCF_004965515.1_ASM496551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e6cf91e-5c3c-404d-9fcc-def8780f1cda/dqc_reference/reference_markers_gtdb.fasta -out GCF_004965515.1_ASM496551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:37,410] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:37,414] [INFO] Selected 19 target genomes.
[2024-01-24 12:24:37,414] [INFO] Target genome list was writen to GCF_004965515.1_ASM496551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:37,424] [INFO] Task started: fastANI
[2024-01-24 12:24:37,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg17420e2e-ea74-4b74-9ebd-47597953fb53/GCF_004965515.1_ASM496551v1_genomic.fna.gz --refList GCF_004965515.1_ASM496551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004965515.1_ASM496551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:48,821] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:48,835] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:48,835] [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_004965515.1	s__Alteraurantiacibacter aquimixticola	100.0	1143	1143	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_009827405.1	s__Alteraurantiacibacter aestuarii	81.0708	498	1143	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	80.3826	618	1143	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	80.0028	540	1143	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	79.9442	546	1143	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	79.793	466	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	79.7287	483	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	79.608	540	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	79.55	464	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	79.4978	516	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.4288	451	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_004114695.1	s__Parerythrobacter sp004114695	79.3591	418	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	79.328	508	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002341345.1	s__Alteraurantiacibacter sp002341345	79.3074	362	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	79.2435	390	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_014359685.1	s__Croceibacterium sp014359685	79.1533	269	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.1011	422	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828065.1	s__Croceibacterium soli	79.0099	454	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	78.9562	458	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:48,838] [INFO] GTDB search result was written to GCF_004965515.1_ASM496551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:48,839] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:48,843] [INFO] DFAST_QC result json was written to GCF_004965515.1_ASM496551v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:48,843] [INFO] DFAST_QC completed!
[2024-01-24 12:24:48,843] [INFO] Total running time: 0h1m14s