[2024-01-25 17:42:20,405] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:20,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:20,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg807b82bf-ad30-45b2-bb03-708097ad986d/dqc_reference
[2024-01-25 17:42:21,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:21,577] [INFO] Task started: Prodigal
[2024-01-25 17:42:21,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg67021b69-e85f-4535-8e4b-a345c2477270/GCF_009828095.1_ASM982809v1_genomic.fna.gz | prodigal -d GCF_009828095.1_ASM982809v1_genomic.fna/cds.fna -a GCF_009828095.1_ASM982809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:29,616] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:29,616] [INFO] Task started: HMMsearch
[2024-01-25 17:42:29,616] [INFO] Running command: hmmsearch --tblout GCF_009828095.1_ASM982809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg807b82bf-ad30-45b2-bb03-708097ad986d/dqc_reference/reference_markers.hmm GCF_009828095.1_ASM982809v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:29,816] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:29,817] [INFO] Found 6/6 markers.
[2024-01-25 17:42:29,842] [INFO] Query marker FASTA was written to GCF_009828095.1_ASM982809v1_genomic.fna/markers.fasta
[2024-01-25 17:42:29,843] [INFO] Task started: Blastn
[2024-01-25 17:42:29,843] [INFO] Running command: blastn -query GCF_009828095.1_ASM982809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg807b82bf-ad30-45b2-bb03-708097ad986d/dqc_reference/reference_markers.fasta -out GCF_009828095.1_ASM982809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:30,605] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:30,609] [INFO] Selected 19 target genomes.
[2024-01-25 17:42:30,609] [INFO] Target genome list was writen to GCF_009828095.1_ASM982809v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:30,626] [INFO] Task started: fastANI
[2024-01-25 17:42:30,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg67021b69-e85f-4535-8e4b-a345c2477270/GCF_009828095.1_ASM982809v1_genomic.fna.gz --refList GCF_009828095.1_ASM982809v1_genomic.fna/target_genomes.txt --output GCF_009828095.1_ASM982809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:41,715] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:41,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg807b82bf-ad30-45b2-bb03-708097ad986d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:41,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg807b82bf-ad30-45b2-bb03-708097ad986d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:41,728] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:41,728] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:41,728] [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
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	100.0	960	961	95	conclusive
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	78.7195	402	961	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	78.3455	345	961	95	below_threshold
Pontixanthobacter gangjinensis	strain=JCM 17802	GCA_009827545.1	1028742	1028742	type	True	78.3224	336	961	95	below_threshold
Pontixanthobacter aestiaquae	strain=KCTC 42006	GCA_009827455.1	1509367	1509367	type	True	78.2862	378	961	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	78.149	328	961	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.1022	329	961	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.0986	328	961	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	78.016	188	961	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.9504	273	961	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.9019	325	961	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.8505	257	961	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	77.8351	305	961	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.8205	306	961	95	below_threshold
Pontixanthobacter rizhaonensis	strain=RZ02	GCA_012972675.1	2730337	2730337	type	True	77.7953	278	961	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.7914	247	961	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	77.7571	228	961	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.7558	272	961	95	below_threshold
Altericroceibacterium endophyticum	strain=LMG 29518	GCA_009827595.1	1808508	1808508	type	True	77.1886	190	961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:41,729] [INFO] DFAST Taxonomy check result was written to GCF_009828095.1_ASM982809v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:41,730] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:41,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:41,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg807b82bf-ad30-45b2-bb03-708097ad986d/dqc_reference/checkm_data
[2024-01-25 17:42:41,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:41,762] [INFO] Task started: CheckM
[2024-01-25 17:42:41,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828095.1_ASM982809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828095.1_ASM982809v1_genomic.fna/checkm_input GCF_009828095.1_ASM982809v1_genomic.fna/checkm_result
[2024-01-25 17:43:08,380] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:08,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:08,397] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:08,397] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:08,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828095.1_ASM982809v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:08,398] [INFO] Task started: Blastn
[2024-01-25 17:43:08,398] [INFO] Running command: blastn -query GCF_009828095.1_ASM982809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg807b82bf-ad30-45b2-bb03-708097ad986d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828095.1_ASM982809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:09,917] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:09,920] [INFO] Selected 19 target genomes.
[2024-01-25 17:43:09,921] [INFO] Target genome list was writen to GCF_009828095.1_ASM982809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:09,938] [INFO] Task started: fastANI
[2024-01-25 17:43:09,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg67021b69-e85f-4535-8e4b-a345c2477270/GCF_009828095.1_ASM982809v1_genomic.fna.gz --refList GCF_009828095.1_ASM982809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828095.1_ASM982809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:21,629] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:21,644] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:21,644] [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_009828095.1	s__Pontixanthobacter luteolus	100.0	960	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009827395.1	s__Pontixanthobacter aquaemixtae	78.7459	399	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.5792	406	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	78.3859	352	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	78.3455	345	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827545.1	s__Pontixanthobacter gangjinensis	78.3224	336	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827455.1	s__Pontixanthobacter aestiaquae	78.2758	379	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017812015.1	s__Pontixanthobacter sp017812015	78.2393	369	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344885.1	s__ZODW24 sp003344885	78.1665	245	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__ZODW24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	78.1388	329	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.1022	329	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177715.1	s__Erythrobacter xiamenensis	78.0656	334	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	77.9185	262	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	77.9019	325	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002870965.1	s__Tsuneonella flava	77.8966	242	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	99.01	98.03	0.92	0.87	3	-
GCA_014763545.1	s__JACXVD01 sp014763545	77.7677	312	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	77.7558	272	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013370205.1	s__Actirhodobacter atriluteus	77.5764	251	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827595.1	s__Altericroceibacterium endophyticum	77.2024	189	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:21,657] [INFO] GTDB search result was written to GCF_009828095.1_ASM982809v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:21,658] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:21,661] [INFO] DFAST_QC result json was written to GCF_009828095.1_ASM982809v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:21,661] [INFO] DFAST_QC completed!
[2024-01-25 17:43:21,661] [INFO] Total running time: 0h1m1s