[2024-01-25 17:36:20,826] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:20,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:20,827] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0c4c6d8-4ffc-4f32-867c-b782c21ff571/dqc_reference
[2024-01-25 17:36:21,931] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:21,933] [INFO] Task started: Prodigal
[2024-01-25 17:36:21,933] [INFO] Running command: gunzip -c /var/lib/cwl/stg80f9010d-ff5e-44be-8067-c02a29024521/GCF_009827335.1_ASM982733v1_genomic.fna.gz | prodigal -d GCF_009827335.1_ASM982733v1_genomic.fna/cds.fna -a GCF_009827335.1_ASM982733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:30,142] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:30,142] [INFO] Task started: HMMsearch
[2024-01-25 17:36:30,142] [INFO] Running command: hmmsearch --tblout GCF_009827335.1_ASM982733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0c4c6d8-4ffc-4f32-867c-b782c21ff571/dqc_reference/reference_markers.hmm GCF_009827335.1_ASM982733v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:30,346] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:30,347] [INFO] Found 6/6 markers.
[2024-01-25 17:36:30,374] [INFO] Query marker FASTA was written to GCF_009827335.1_ASM982733v1_genomic.fna/markers.fasta
[2024-01-25 17:36:30,374] [INFO] Task started: Blastn
[2024-01-25 17:36:30,374] [INFO] Running command: blastn -query GCF_009827335.1_ASM982733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c4c6d8-4ffc-4f32-867c-b782c21ff571/dqc_reference/reference_markers.fasta -out GCF_009827335.1_ASM982733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:31,174] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:31,177] [INFO] Selected 17 target genomes.
[2024-01-25 17:36:31,177] [INFO] Target genome list was writen to GCF_009827335.1_ASM982733v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:31,196] [INFO] Task started: fastANI
[2024-01-25 17:36:31,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f9010d-ff5e-44be-8067-c02a29024521/GCF_009827335.1_ASM982733v1_genomic.fna.gz --refList GCF_009827335.1_ASM982733v1_genomic.fna/target_genomes.txt --output GCF_009827335.1_ASM982733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:41,602] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:41,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0c4c6d8-4ffc-4f32-867c-b782c21ff571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:41,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0c4c6d8-4ffc-4f32-867c-b782c21ff571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:41,614] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:36:41,614] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:41,614] [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 arachoides	strain=RC4-10-4	GCA_009827335.1	1850444	1850444	type	True	100.0	980	980	95	conclusive
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	99.9995	978	980	95	conclusive
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	84.832	732	980	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	80.2307	544	980	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	79.8772	535	980	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	79.4611	396	980	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	79.227	438	980	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.0899	430	980	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.8993	296	980	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.8952	377	980	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.8351	386	980	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.8053	350	980	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.7443	372	980	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.5953	265	980	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.4412	351	980	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	78.361	374	980	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.9331	336	980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:41,615] [INFO] DFAST Taxonomy check result was written to GCF_009827335.1_ASM982733v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:41,616] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:41,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:41,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0c4c6d8-4ffc-4f32-867c-b782c21ff571/dqc_reference/checkm_data
[2024-01-25 17:36:41,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:41,648] [INFO] Task started: CheckM
[2024-01-25 17:36:41,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827335.1_ASM982733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827335.1_ASM982733v1_genomic.fna/checkm_input GCF_009827335.1_ASM982733v1_genomic.fna/checkm_result
[2024-01-25 17:37:09,117] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:09,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:09,138] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:09,138] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:09,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827335.1_ASM982733v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:09,139] [INFO] Task started: Blastn
[2024-01-25 17:37:09,139] [INFO] Running command: blastn -query GCF_009827335.1_ASM982733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c4c6d8-4ffc-4f32-867c-b782c21ff571/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827335.1_ASM982733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:10,529] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:10,532] [INFO] Selected 20 target genomes.
[2024-01-25 17:37:10,532] [INFO] Target genome list was writen to GCF_009827335.1_ASM982733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:10,541] [INFO] Task started: fastANI
[2024-01-25 17:37:10,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f9010d-ff5e-44be-8067-c02a29024521/GCF_009827335.1_ASM982733v1_genomic.fna.gz --refList GCF_009827335.1_ASM982733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827335.1_ASM982733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:23,007] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:23,019] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:23,020] [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_009827335.1	s__Alteraurantiacibacter arachoides	100.0	980	980	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_001010945.1	s__Alteraurantiacibacter luteus	84.832	732	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	80.2363	543	980	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	79.8818	534	980	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	79.8243	477	980	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	79.6198	437	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	79.4335	499	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	79.2162	392	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.0859	431	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	79.0657	492	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698205.1	s__Tsuneonella dongtanensis	79.0261	339	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	78.9898	400	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793865.1	s__Qipengyuania sp016793865	78.9806	329	980	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	78.9381	392	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.9064	376	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	78.794	376	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_009827315.1	s__Qipengyuania gaetbuli	78.7394	373	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279825.1	s__Croceibacterium sp002279825	78.6391	391	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCF_018205975.1	s__Erythrobacter sp018205975	78.4872	348	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	78.3885	351	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:23,021] [INFO] GTDB search result was written to GCF_009827335.1_ASM982733v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:23,022] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:23,026] [INFO] DFAST_QC result json was written to GCF_009827335.1_ASM982733v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:23,026] [INFO] DFAST_QC completed!
[2024-01-25 17:37:23,026] [INFO] Total running time: 0h1m2s