[2024-01-25 18:46:20,574] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:20,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:20,575] [INFO] DQC Reference Directory: /var/lib/cwl/stgda43004a-13d3-41c2-aa91-bceab8c9d548/dqc_reference
[2024-01-25 18:46:21,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:21,764] [INFO] Task started: Prodigal
[2024-01-25 18:46:21,764] [INFO] Running command: gunzip -c /var/lib/cwl/stgb53cd15c-4272-4140-8d78-5417b35a8325/GCF_025154015.1_ASM2515401v1_genomic.fna.gz | prodigal -d GCF_025154015.1_ASM2515401v1_genomic.fna/cds.fna -a GCF_025154015.1_ASM2515401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:29,398] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:29,399] [INFO] Task started: HMMsearch
[2024-01-25 18:46:29,399] [INFO] Running command: hmmsearch --tblout GCF_025154015.1_ASM2515401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda43004a-13d3-41c2-aa91-bceab8c9d548/dqc_reference/reference_markers.hmm GCF_025154015.1_ASM2515401v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:29,601] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:29,602] [INFO] Found 6/6 markers.
[2024-01-25 18:46:29,628] [INFO] Query marker FASTA was written to GCF_025154015.1_ASM2515401v1_genomic.fna/markers.fasta
[2024-01-25 18:46:29,628] [INFO] Task started: Blastn
[2024-01-25 18:46:29,629] [INFO] Running command: blastn -query GCF_025154015.1_ASM2515401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda43004a-13d3-41c2-aa91-bceab8c9d548/dqc_reference/reference_markers.fasta -out GCF_025154015.1_ASM2515401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:30,577] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:30,579] [INFO] Selected 16 target genomes.
[2024-01-25 18:46:30,579] [INFO] Target genome list was writen to GCF_025154015.1_ASM2515401v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:30,592] [INFO] Task started: fastANI
[2024-01-25 18:46:30,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgb53cd15c-4272-4140-8d78-5417b35a8325/GCF_025154015.1_ASM2515401v1_genomic.fna.gz --refList GCF_025154015.1_ASM2515401v1_genomic.fna/target_genomes.txt --output GCF_025154015.1_ASM2515401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:40,087] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:40,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda43004a-13d3-41c2-aa91-bceab8c9d548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:40,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda43004a-13d3-41c2-aa91-bceab8c9d548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:40,098] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:46:40,098] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:46:40,098] [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 amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	82.4366	624	994	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	82.2041	613	994	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	82.0309	610	994	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	81.9031	614	994	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	80.8061	539	994	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	80.5982	487	994	95	below_threshold
Tsuneonella aeria	strain=100921-2	GCA_009827495.1	1837929	1837929	type	True	80.5308	513	994	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	80.4461	499	994	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	80.4237	537	994	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.3724	490	994	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.4919	437	994	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.4155	372	994	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	79.2404	398	994	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	79.1095	402	994	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.9577	406	994	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	78.5681	408	994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:40,100] [INFO] DFAST Taxonomy check result was written to GCF_025154015.1_ASM2515401v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:40,100] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:40,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:40,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda43004a-13d3-41c2-aa91-bceab8c9d548/dqc_reference/checkm_data
[2024-01-25 18:46:40,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:40,134] [INFO] Task started: CheckM
[2024-01-25 18:46:40,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025154015.1_ASM2515401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025154015.1_ASM2515401v1_genomic.fna/checkm_input GCF_025154015.1_ASM2515401v1_genomic.fna/checkm_result
[2024-01-25 18:47:05,986] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:05,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:06,011] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:06,012] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:06,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025154015.1_ASM2515401v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:06,013] [INFO] Task started: Blastn
[2024-01-25 18:47:06,013] [INFO] Running command: blastn -query GCF_025154015.1_ASM2515401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda43004a-13d3-41c2-aa91-bceab8c9d548/dqc_reference/reference_markers_gtdb.fasta -out GCF_025154015.1_ASM2515401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:07,907] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:07,911] [INFO] Selected 16 target genomes.
[2024-01-25 18:47:07,911] [INFO] Target genome list was writen to GCF_025154015.1_ASM2515401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:07,923] [INFO] Task started: fastANI
[2024-01-25 18:47:07,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgb53cd15c-4272-4140-8d78-5417b35a8325/GCF_025154015.1_ASM2515401v1_genomic.fna.gz --refList GCF_025154015.1_ASM2515401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025154015.1_ASM2515401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:17,998] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:18,008] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:47:18,008] [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_001698205.1	s__Tsuneonella dongtanensis	83.0597	648	994	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	82.4241	625	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958625.1	s__Tsuneonella rigui	82.2139	612	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441535.1	s__Tsuneonella troitsensis	82.0309	610	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014644315.1	s__Tsuneonella deserti	80.7909	540	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	80.69	502	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	80.6105	485	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269345.1	s__Tsuneonella mangrovi	80.5968	488	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827495.1	s__Tsuneonella aeria	80.543	512	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	80.4576	498	994	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	79.8304	412	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.5393	465	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_015529805.1	s__Qipengyuania soli	79.4446	451	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	79.2527	397	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000422985.1	s__Erythrobacter cryptus	78.5691	408	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000264945.2	s__Sphingobium indicum	77.779	244	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:18,009] [INFO] GTDB search result was written to GCF_025154015.1_ASM2515401v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:18,010] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:18,013] [INFO] DFAST_QC result json was written to GCF_025154015.1_ASM2515401v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:18,013] [INFO] DFAST_QC completed!
[2024-01-25 18:47:18,014] [INFO] Total running time: 0h0m57s