[2024-01-25 19:09:05,466] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:05,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:05,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgccb5eec8-0e9d-4327-b5cd-6200c2f4aba5/dqc_reference
[2024-01-25 19:09:06,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:06,600] [INFO] Task started: Prodigal
[2024-01-25 19:09:06,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg1465f5e4-4216-4990-bdba-15ab870d7cc8/GCF_001010925.1_ASM101092v1_genomic.fna.gz | prodigal -d GCF_001010925.1_ASM101092v1_genomic.fna/cds.fna -a GCF_001010925.1_ASM101092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:14,421] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:14,421] [INFO] Task started: HMMsearch
[2024-01-25 19:09:14,421] [INFO] Running command: hmmsearch --tblout GCF_001010925.1_ASM101092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccb5eec8-0e9d-4327-b5cd-6200c2f4aba5/dqc_reference/reference_markers.hmm GCF_001010925.1_ASM101092v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:14,616] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:14,618] [INFO] Found 6/6 markers.
[2024-01-25 19:09:14,646] [INFO] Query marker FASTA was written to GCF_001010925.1_ASM101092v1_genomic.fna/markers.fasta
[2024-01-25 19:09:14,646] [INFO] Task started: Blastn
[2024-01-25 19:09:14,646] [INFO] Running command: blastn -query GCF_001010925.1_ASM101092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccb5eec8-0e9d-4327-b5cd-6200c2f4aba5/dqc_reference/reference_markers.fasta -out GCF_001010925.1_ASM101092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:15,487] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:15,490] [INFO] Selected 17 target genomes.
[2024-01-25 19:09:15,490] [INFO] Target genome list was writen to GCF_001010925.1_ASM101092v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:15,533] [INFO] Task started: fastANI
[2024-01-25 19:09:15,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg1465f5e4-4216-4990-bdba-15ab870d7cc8/GCF_001010925.1_ASM101092v1_genomic.fna.gz --refList GCF_001010925.1_ASM101092v1_genomic.fna/target_genomes.txt --output GCF_001010925.1_ASM101092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:26,557] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:26,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccb5eec8-0e9d-4327-b5cd-6200c2f4aba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:26,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccb5eec8-0e9d-4327-b5cd-6200c2f4aba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:26,567] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:09:26,568] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:26,568] [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
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	100.0	907	907	95	conclusive
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	99.9957	906	907	95	conclusive
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	80.1451	545	907	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	79.9213	540	907	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	79.863	503	907	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	79.4743	481	907	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	79.334	496	907	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.8131	373	907	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.7199	336	907	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.6895	367	907	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.5704	323	907	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	78.5445	319	907	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.4678	355	907	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.4407	272	907	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.3069	345	907	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.2722	349	907	95	below_threshold
Croceicoccus mobilis	strain=CGMCC 1.15360	GCA_014642595.1	1703339	1703339	type	True	77.957	273	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:26,569] [INFO] DFAST Taxonomy check result was written to GCF_001010925.1_ASM101092v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:26,570] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:26,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:26,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccb5eec8-0e9d-4327-b5cd-6200c2f4aba5/dqc_reference/checkm_data
[2024-01-25 19:09:26,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:26,600] [INFO] Task started: CheckM
[2024-01-25 19:09:26,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001010925.1_ASM101092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001010925.1_ASM101092v1_genomic.fna/checkm_input GCF_001010925.1_ASM101092v1_genomic.fna/checkm_result
[2024-01-25 19:09:52,336] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:52,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:52,356] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:52,357] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:52,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001010925.1_ASM101092v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:52,357] [INFO] Task started: Blastn
[2024-01-25 19:09:52,357] [INFO] Running command: blastn -query GCF_001010925.1_ASM101092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccb5eec8-0e9d-4327-b5cd-6200c2f4aba5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001010925.1_ASM101092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:53,940] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:53,943] [INFO] Selected 15 target genomes.
[2024-01-25 19:09:53,943] [INFO] Target genome list was writen to GCF_001010925.1_ASM101092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:53,958] [INFO] Task started: fastANI
[2024-01-25 19:09:53,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg1465f5e4-4216-4990-bdba-15ab870d7cc8/GCF_001010925.1_ASM101092v1_genomic.fna.gz --refList GCF_001010925.1_ASM101092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001010925.1_ASM101092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:03,014] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:03,023] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:03,024] [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_001886695.1	s__Alteraurantiacibacter gangjinensis	99.9957	906	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003605195.1	s__Alteraurantiacibacter odishensis	80.1603	543	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	79.9884	531	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	79.9013	542	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	79.8474	504	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	79.759	543	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019885.1	s__Alteraurantiacibacter sp016019885	79.4743	481	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	79.334	496	907	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	79.2182	441	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	79.1035	423	907	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	78.842	370	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	78.7199	336	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	78.5792	319	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	78.5173	309	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.3173	344	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:03,027] [INFO] GTDB search result was written to GCF_001010925.1_ASM101092v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:03,028] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:03,031] [INFO] DFAST_QC result json was written to GCF_001010925.1_ASM101092v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:03,032] [INFO] DFAST_QC completed!
[2024-01-25 19:10:03,032] [INFO] Total running time: 0h0m58s