[2024-01-24 14:28:08,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f648c12-70a2-44f5-975a-661a321071a6/dqc_reference
[2024-01-24 14:28:10,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,420] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,420] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd96983a-aa78-4b23-8132-e6550e6f1114/GCF_009827545.1_ASM982754v1_genomic.fna.gz | prodigal -d GCF_009827545.1_ASM982754v1_genomic.fna/cds.fna -a GCF_009827545.1_ASM982754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:19,967] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:19,967] [INFO] Task started: HMMsearch
[2024-01-24 14:28:19,968] [INFO] Running command: hmmsearch --tblout GCF_009827545.1_ASM982754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f648c12-70a2-44f5-975a-661a321071a6/dqc_reference/reference_markers.hmm GCF_009827545.1_ASM982754v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:20,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:20,246] [INFO] Found 6/6 markers.
[2024-01-24 14:28:20,279] [INFO] Query marker FASTA was written to GCF_009827545.1_ASM982754v1_genomic.fna/markers.fasta
[2024-01-24 14:28:20,280] [INFO] Task started: Blastn
[2024-01-24 14:28:20,280] [INFO] Running command: blastn -query GCF_009827545.1_ASM982754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f648c12-70a2-44f5-975a-661a321071a6/dqc_reference/reference_markers.fasta -out GCF_009827545.1_ASM982754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:20,976] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:20,979] [INFO] Selected 19 target genomes.
[2024-01-24 14:28:20,979] [INFO] Target genome list was writen to GCF_009827545.1_ASM982754v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:20,993] [INFO] Task started: fastANI
[2024-01-24 14:28:20,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd96983a-aa78-4b23-8132-e6550e6f1114/GCF_009827545.1_ASM982754v1_genomic.fna.gz --refList GCF_009827545.1_ASM982754v1_genomic.fna/target_genomes.txt --output GCF_009827545.1_ASM982754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:34,242] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:34,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f648c12-70a2-44f5-975a-661a321071a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:34,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f648c12-70a2-44f5-975a-661a321071a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:34,257] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:34,257] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:34,257] [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
Pontixanthobacter gangjinensis	strain=JCM 17802	GCA_009827545.1	1028742	1028742	type	True	100.0	962	962	95	conclusive
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	78.486	326	962	95	below_threshold
Pontixanthobacter aestiaquae	strain=KCTC 42006	GCA_009827455.1	1509367	1509367	type	True	78.4481	334	962	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	78.2195	353	962	95	below_threshold
Pontixanthobacter rizhaonensis	strain=RZ02	GCA_012972675.1	2730337	2730337	type	True	78.0116	262	962	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	77.7675	198	962	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	77.5688	112	962	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	77.5615	217	962	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	77.11	104	962	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	77.0209	146	962	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.016	143	962	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	76.9392	145	962	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	76.8945	142	962	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.884	134	962	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	76.859	164	962	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	76.7959	106	962	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	76.7835	90	962	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	76.7751	122	962	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	76.4479	87	962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:34,260] [INFO] DFAST Taxonomy check result was written to GCF_009827545.1_ASM982754v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:34,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:34,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:34,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f648c12-70a2-44f5-975a-661a321071a6/dqc_reference/checkm_data
[2024-01-24 14:28:34,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:34,296] [INFO] Task started: CheckM
[2024-01-24 14:28:34,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827545.1_ASM982754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827545.1_ASM982754v1_genomic.fna/checkm_input GCF_009827545.1_ASM982754v1_genomic.fna/checkm_result
[2024-01-24 14:29:08,427] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:08,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:08,446] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:08,447] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:08,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827545.1_ASM982754v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:08,448] [INFO] Task started: Blastn
[2024-01-24 14:29:08,448] [INFO] Running command: blastn -query GCF_009827545.1_ASM982754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f648c12-70a2-44f5-975a-661a321071a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827545.1_ASM982754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:09,414] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:09,421] [INFO] Selected 17 target genomes.
[2024-01-24 14:29:09,421] [INFO] Target genome list was writen to GCF_009827545.1_ASM982754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:09,446] [INFO] Task started: fastANI
[2024-01-24 14:29:09,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd96983a-aa78-4b23-8132-e6550e6f1114/GCF_009827545.1_ASM982754v1_genomic.fna.gz --refList GCF_009827545.1_ASM982754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827545.1_ASM982754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:18,258] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:18,277] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:18,277] [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_009827545.1	s__Pontixanthobacter gangjinensis	100.0	962	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009828095.1	s__Pontixanthobacter luteolus	78.486	326	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827455.1	s__Pontixanthobacter aestiaquae	78.4481	334	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017812015.1	s__Pontixanthobacter sp017812015	78.3551	330	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827395.1	s__Pontixanthobacter aquaemixtae	78.2195	353	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012972675.1	s__Pontixanthobacter rizhaonensis	78.0083	261	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	77.7675	198	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	77.6241	217	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	77.1108	190	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	77.1076	146	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	76.9021	136	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	76.8472	135	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_014763545.1	s__JACXVD01 sp014763545	76.7579	156	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	76.7214	92	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	76.5614	110	962	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	76.4209	129	962	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	76.243	79	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:18,279] [INFO] GTDB search result was written to GCF_009827545.1_ASM982754v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:18,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:18,284] [INFO] DFAST_QC result json was written to GCF_009827545.1_ASM982754v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:18,284] [INFO] DFAST_QC completed!
[2024-01-24 14:29:18,284] [INFO] Total running time: 0h1m10s