[2024-01-24 15:26:39,816] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1f147d6-95aa-4626-8c52-d5486aa2f148/dqc_reference
[2024-01-24 15:26:41,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,224] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,224] [INFO] Running command: gunzip -c /var/lib/cwl/stge0351d81-c301-4579-aace-6bacdfd32eed/GCF_009372075.1_ASM937207v1_genomic.fna.gz | prodigal -d GCF_009372075.1_ASM937207v1_genomic.fna/cds.fna -a GCF_009372075.1_ASM937207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:51,994] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:51,995] [INFO] Task started: HMMsearch
[2024-01-24 15:26:51,995] [INFO] Running command: hmmsearch --tblout GCF_009372075.1_ASM937207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1f147d6-95aa-4626-8c52-d5486aa2f148/dqc_reference/reference_markers.hmm GCF_009372075.1_ASM937207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:52,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:52,261] [INFO] Found 6/6 markers.
[2024-01-24 15:26:52,295] [INFO] Query marker FASTA was written to GCF_009372075.1_ASM937207v1_genomic.fna/markers.fasta
[2024-01-24 15:26:52,295] [INFO] Task started: Blastn
[2024-01-24 15:26:52,296] [INFO] Running command: blastn -query GCF_009372075.1_ASM937207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1f147d6-95aa-4626-8c52-d5486aa2f148/dqc_reference/reference_markers.fasta -out GCF_009372075.1_ASM937207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:53,214] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:53,223] [INFO] Selected 15 target genomes.
[2024-01-24 15:26:53,224] [INFO] Target genome list was writen to GCF_009372075.1_ASM937207v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:53,235] [INFO] Task started: fastANI
[2024-01-24 15:26:53,235] [INFO] Running command: fastANI --query /var/lib/cwl/stge0351d81-c301-4579-aace-6bacdfd32eed/GCF_009372075.1_ASM937207v1_genomic.fna.gz --refList GCF_009372075.1_ASM937207v1_genomic.fna/target_genomes.txt --output GCF_009372075.1_ASM937207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:03,827] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:03,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1f147d6-95aa-4626-8c52-d5486aa2f148/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:03,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1f147d6-95aa-4626-8c52-d5486aa2f148/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:03,840] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:27:03,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:03,841] [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
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	100.0	1118	1118	95	conclusive
Polymorphobacter fuscus	strain=D40P	GCA_009372075.1	1439888	1439888	type	True	100.0	1118	1118	95	conclusive
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	99.9842	1116	1118	95	conclusive
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	80.711	580	1118	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	79.2895	488	1118	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	79.2839	441	1118	95	below_threshold
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	78.9986	356	1118	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	78.924	400	1118	95	below_threshold
Sandarakinorhabdus limnophila	strain=DSM 17366	GCA_000420765.1	210512	210512	type	True	78.5811	374	1118	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	77.4137	158	1118	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.2395	315	1118	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	77.192	178	1118	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.0565	312	1118	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	76.959	285	1118	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.7346	335	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:03,842] [INFO] DFAST Taxonomy check result was written to GCF_009372075.1_ASM937207v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:03,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:03,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:03,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1f147d6-95aa-4626-8c52-d5486aa2f148/dqc_reference/checkm_data
[2024-01-24 15:27:03,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:03,884] [INFO] Task started: CheckM
[2024-01-24 15:27:03,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009372075.1_ASM937207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009372075.1_ASM937207v1_genomic.fna/checkm_input GCF_009372075.1_ASM937207v1_genomic.fna/checkm_result
[2024-01-24 15:27:42,540] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:42,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:42,560] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:42,561] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:42,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009372075.1_ASM937207v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:42,562] [INFO] Task started: Blastn
[2024-01-24 15:27:42,562] [INFO] Running command: blastn -query GCF_009372075.1_ASM937207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1f147d6-95aa-4626-8c52-d5486aa2f148/dqc_reference/reference_markers_gtdb.fasta -out GCF_009372075.1_ASM937207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:44,167] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:44,170] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:44,171] [INFO] Target genome list was writen to GCF_009372075.1_ASM937207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:44,181] [INFO] Task started: fastANI
[2024-01-24 15:27:44,181] [INFO] Running command: fastANI --query /var/lib/cwl/stge0351d81-c301-4579-aace-6bacdfd32eed/GCF_009372075.1_ASM937207v1_genomic.fna.gz --refList GCF_009372075.1_ASM937207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009372075.1_ASM937207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:52,476] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:52,492] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:52,492] [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_011927825.1	s__Polymorphobacter fuscus	99.9842	1116	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.98	99.98	1.00	1.00	3	conclusive
GCA_003241875.1	s__Polymorphobacter sp003241875	82.216	665	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256005.1	s__Polymorphobacter sp002256005	81.7017	611	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298745.1	s__Polymorphobacter sp013298745	81.4101	463	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903939555.1	s__Polymorphobacter sp903939555	80.9305	438	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	98.54	98.06	0.84	0.82	4	-
GCF_014643455.1	s__Polymorphobacter glacialis	80.705	581	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001295935.1	s__Polymorphobacter sp001295935	80.2026	561	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423025.1	s__Polymorphobacter sp002423025	79.3257	467	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205635.1	s__Polymorphobacter multimanifer	79.2895	488	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.78	99.78	0.99	0.99	2	-
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	78.8283	419	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377915.1	s__Tardiphaga sp014377915	75.3258	119	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:52,494] [INFO] GTDB search result was written to GCF_009372075.1_ASM937207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:52,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:52,498] [INFO] DFAST_QC result json was written to GCF_009372075.1_ASM937207v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:52,498] [INFO] DFAST_QC completed!
[2024-01-24 15:27:52,498] [INFO] Total running time: 0h1m13s