[2024-01-24 15:03:14,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:14,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:14,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0f0119e-0b7f-4cca-beb2-a684b7e917d9/dqc_reference
[2024-01-24 15:03:15,974] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:15,975] [INFO] Task started: Prodigal
[2024-01-24 15:03:15,975] [INFO] Running command: gunzip -c /var/lib/cwl/stg1fe9a30d-e5f9-4f33-b571-a673c0dd1fb7/GCF_009827405.1_ASM982740v1_genomic.fna.gz | prodigal -d GCF_009827405.1_ASM982740v1_genomic.fna/cds.fna -a GCF_009827405.1_ASM982740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:23,954] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:23,954] [INFO] Task started: HMMsearch
[2024-01-24 15:03:23,954] [INFO] Running command: hmmsearch --tblout GCF_009827405.1_ASM982740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0f0119e-0b7f-4cca-beb2-a684b7e917d9/dqc_reference/reference_markers.hmm GCF_009827405.1_ASM982740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:24,168] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:24,169] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1fe9a30d-e5f9-4f33-b571-a673c0dd1fb7/GCF_009827405.1_ASM982740v1_genomic.fna.gz]
[2024-01-24 15:03:24,191] [INFO] Query marker FASTA was written to GCF_009827405.1_ASM982740v1_genomic.fna/markers.fasta
[2024-01-24 15:03:24,192] [INFO] Task started: Blastn
[2024-01-24 15:03:24,192] [INFO] Running command: blastn -query GCF_009827405.1_ASM982740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0f0119e-0b7f-4cca-beb2-a684b7e917d9/dqc_reference/reference_markers.fasta -out GCF_009827405.1_ASM982740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:24,882] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:24,886] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:24,886] [INFO] Target genome list was writen to GCF_009827405.1_ASM982740v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:24,897] [INFO] Task started: fastANI
[2024-01-24 15:03:24,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fe9a30d-e5f9-4f33-b571-a673c0dd1fb7/GCF_009827405.1_ASM982740v1_genomic.fna.gz --refList GCF_009827405.1_ASM982740v1_genomic.fna/target_genomes.txt --output GCF_009827405.1_ASM982740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:33,207] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:33,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0f0119e-0b7f-4cca-beb2-a684b7e917d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:33,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0f0119e-0b7f-4cca-beb2-a684b7e917d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:33,221] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:33,221] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:33,221] [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
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	100.0	744	745	95	conclusive
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	79.5511	379	745	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	78.9427	314	745	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	78.9226	331	745	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	78.8776	276	745	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	78.8228	275	745	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	78.7985	289	745	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.771	325	745	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	78.7141	245	745	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.6422	288	745	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	78.5028	244	745	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	78.4755	237	745	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.2748	207	745	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.0935	181	745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:33,223] [INFO] DFAST Taxonomy check result was written to GCF_009827405.1_ASM982740v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:33,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:33,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:33,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0f0119e-0b7f-4cca-beb2-a684b7e917d9/dqc_reference/checkm_data
[2024-01-24 15:03:33,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:33,250] [INFO] Task started: CheckM
[2024-01-24 15:03:33,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827405.1_ASM982740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827405.1_ASM982740v1_genomic.fna/checkm_input GCF_009827405.1_ASM982740v1_genomic.fna/checkm_result
[2024-01-24 15:04:00,989] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:00,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:01,015] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:01,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:01,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827405.1_ASM982740v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:01,016] [INFO] Task started: Blastn
[2024-01-24 15:04:01,016] [INFO] Running command: blastn -query GCF_009827405.1_ASM982740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0f0119e-0b7f-4cca-beb2-a684b7e917d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827405.1_ASM982740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:01,822] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:01,826] [INFO] Selected 12 target genomes.
[2024-01-24 15:04:01,826] [INFO] Target genome list was writen to GCF_009827405.1_ASM982740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:01,836] [INFO] Task started: fastANI
[2024-01-24 15:04:01,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fe9a30d-e5f9-4f33-b571-a673c0dd1fb7/GCF_009827405.1_ASM982740v1_genomic.fna.gz --refList GCF_009827405.1_ASM982740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827405.1_ASM982740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:10,033] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:10,051] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:10,052] [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_009827405.1	s__Alteraurantiacibacter aestuarii	100.0	744	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	81.1106	483	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	80.0397	437	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	79.5362	341	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	79.5035	383	745	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	79.2229	270	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	79.0749	278	745	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	78.9226	331	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827335.1	s__Alteraurantiacibacter arachoides	78.8767	276	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	78.8614	277	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003660445.1	s__Croceibacterium ferulae	78.6964	246	745	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	78.3127	266	745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:10,053] [INFO] GTDB search result was written to GCF_009827405.1_ASM982740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:10,054] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:10,057] [INFO] DFAST_QC result json was written to GCF_009827405.1_ASM982740v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:10,058] [INFO] DFAST_QC completed!
[2024-01-24 15:04:10,058] [INFO] Total running time: 0h0m55s