[2024-01-25 17:52:20,539] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:20,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:20,541] [INFO] DQC Reference Directory: /var/lib/cwl/stga457c602-faa9-4150-ab60-2f4d305d4c40/dqc_reference
[2024-01-25 17:52:21,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:21,694] [INFO] Task started: Prodigal
[2024-01-25 17:52:21,694] [INFO] Running command: gunzip -c /var/lib/cwl/stgbab29f74-4ad4-4b4e-a1b1-84a92e0bbc73/GCF_009827435.1_ASM982743v1_genomic.fna.gz | prodigal -d GCF_009827435.1_ASM982743v1_genomic.fna/cds.fna -a GCF_009827435.1_ASM982743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:30,947] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:30,947] [INFO] Task started: HMMsearch
[2024-01-25 17:52:30,947] [INFO] Running command: hmmsearch --tblout GCF_009827435.1_ASM982743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga457c602-faa9-4150-ab60-2f4d305d4c40/dqc_reference/reference_markers.hmm GCF_009827435.1_ASM982743v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:31,140] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:31,141] [INFO] Found 6/6 markers.
[2024-01-25 17:52:31,171] [INFO] Query marker FASTA was written to GCF_009827435.1_ASM982743v1_genomic.fna/markers.fasta
[2024-01-25 17:52:31,171] [INFO] Task started: Blastn
[2024-01-25 17:52:31,171] [INFO] Running command: blastn -query GCF_009827435.1_ASM982743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga457c602-faa9-4150-ab60-2f4d305d4c40/dqc_reference/reference_markers.fasta -out GCF_009827435.1_ASM982743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:32,142] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:32,145] [INFO] Selected 23 target genomes.
[2024-01-25 17:52:32,145] [INFO] Target genome list was writen to GCF_009827435.1_ASM982743v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:32,159] [INFO] Task started: fastANI
[2024-01-25 17:52:32,160] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab29f74-4ad4-4b4e-a1b1-84a92e0bbc73/GCF_009827435.1_ASM982743v1_genomic.fna.gz --refList GCF_009827435.1_ASM982743v1_genomic.fna/target_genomes.txt --output GCF_009827435.1_ASM982743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:46,871] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:46,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga457c602-faa9-4150-ab60-2f4d305d4c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:46,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga457c602-faa9-4150-ab60-2f4d305d4c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:46,884] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:52:46,885] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:52:46,885] [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
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	80.1292	455	1187	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	80.0163	427	1187	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.9814	425	1187	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	79.9537	414	1187	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.7318	460	1187	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.7124	422	1187	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	79.4004	383	1187	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	79.3797	383	1187	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.3094	431	1187	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.2985	378	1187	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	79.2969	360	1187	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.2959	406	1187	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.244	389	1187	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	79.2338	395	1187	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.0376	372	1187	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	79.0124	411	1187	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.9891	304	1187	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.8544	342	1187	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.8046	353	1187	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	78.8039	350	1187	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.7928	369	1187	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	78.6096	347	1187	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	78.3305	300	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:46,886] [INFO] DFAST Taxonomy check result was written to GCF_009827435.1_ASM982743v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:46,887] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:46,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:46,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga457c602-faa9-4150-ab60-2f4d305d4c40/dqc_reference/checkm_data
[2024-01-25 17:52:46,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:46,925] [INFO] Task started: CheckM
[2024-01-25 17:52:46,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827435.1_ASM982743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827435.1_ASM982743v1_genomic.fna/checkm_input GCF_009827435.1_ASM982743v1_genomic.fna/checkm_result
[2024-01-25 17:53:15,261] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:15,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:15,279] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:15,279] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:15,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827435.1_ASM982743v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:15,280] [INFO] Task started: Blastn
[2024-01-25 17:53:15,281] [INFO] Running command: blastn -query GCF_009827435.1_ASM982743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga457c602-faa9-4150-ab60-2f4d305d4c40/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827435.1_ASM982743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:17,270] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:17,274] [INFO] Selected 20 target genomes.
[2024-01-25 17:53:17,274] [INFO] Target genome list was writen to GCF_009827435.1_ASM982743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:17,293] [INFO] Task started: fastANI
[2024-01-25 17:53:17,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab29f74-4ad4-4b4e-a1b1-84a92e0bbc73/GCF_009827435.1_ASM982743v1_genomic.fna.gz --refList GCF_009827435.1_ASM982743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827435.1_ASM982743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:30,362] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:30,374] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:30,374] [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_009827435.1	s__Croceibacterium salegens	100.0	1184	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011320115.1	s__Croceibacterium segetis	81.1822	641	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828065.1	s__Croceibacterium soli	80.9482	572	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	80.2552	436	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279825.1	s__Croceibacterium sp002279825	80.2303	508	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCF_003958625.1	s__Tsuneonella rigui	80.1829	450	1187	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	79.9537	414	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698205.1	s__Tsuneonella dongtanensis	79.9456	418	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427865.1	s__Croceibacterium sp001427865	79.7291	542	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	79.7277	417	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744315.1	s__Croceibacterium sp017744315	79.6938	506	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	79.569	499	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.4249	450	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_018599195.1	s__Croceibacterium sp018599195	79.3771	449	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644315.1	s__Tsuneonella deserti	79.3024	361	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359685.1	s__Croceibacterium sp014359685	79.1716	270	1187	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	79.0126	411	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742225.1	s__Novosphingobium resinovorum	78.9156	415	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCA_003248395.1	s__Qipengyuania sp003248395	78.5608	266	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305965.1	s__Caenibius sp001305965	78.3375	391	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:30,376] [INFO] GTDB search result was written to GCF_009827435.1_ASM982743v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:30,376] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:30,380] [INFO] DFAST_QC result json was written to GCF_009827435.1_ASM982743v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:30,380] [INFO] DFAST_QC completed!
[2024-01-25 17:53:30,380] [INFO] Total running time: 0h1m10s