[2024-01-24 14:31:00,269] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,272] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f679f6b-67b7-4ce6-8816-b7c84c3055fb/dqc_reference
[2024-01-24 14:31:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,104] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg05e3a001-e7e6-41a7-b8e0-4c039a7723eb/GCF_009827495.1_ASM982749v1_genomic.fna.gz | prodigal -d GCF_009827495.1_ASM982749v1_genomic.fna/cds.fna -a GCF_009827495.1_ASM982749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:09,717] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:09,717] [INFO] Task started: HMMsearch
[2024-01-24 14:31:09,717] [INFO] Running command: hmmsearch --tblout GCF_009827495.1_ASM982749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f679f6b-67b7-4ce6-8816-b7c84c3055fb/dqc_reference/reference_markers.hmm GCF_009827495.1_ASM982749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:09,943] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:09,944] [INFO] Found 6/6 markers.
[2024-01-24 14:31:09,967] [INFO] Query marker FASTA was written to GCF_009827495.1_ASM982749v1_genomic.fna/markers.fasta
[2024-01-24 14:31:09,967] [INFO] Task started: Blastn
[2024-01-24 14:31:09,967] [INFO] Running command: blastn -query GCF_009827495.1_ASM982749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f679f6b-67b7-4ce6-8816-b7c84c3055fb/dqc_reference/reference_markers.fasta -out GCF_009827495.1_ASM982749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:10,759] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:10,761] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:10,762] [INFO] Target genome list was writen to GCF_009827495.1_ASM982749v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:10,768] [INFO] Task started: fastANI
[2024-01-24 14:31:10,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg05e3a001-e7e6-41a7-b8e0-4c039a7723eb/GCF_009827495.1_ASM982749v1_genomic.fna.gz --refList GCF_009827495.1_ASM982749v1_genomic.fna/target_genomes.txt --output GCF_009827495.1_ASM982749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:20,222] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:20,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f679f6b-67b7-4ce6-8816-b7c84c3055fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:20,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f679f6b-67b7-4ce6-8816-b7c84c3055fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:20,233] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:20,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:20,233] [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
Tsuneonella aeria	strain=100921-2	GCA_009827495.1	1837929	1837929	type	True	100.0	916	916	95	conclusive
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	81.0374	535	916	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	80.9797	528	916	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	80.9602	511	916	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	80.8558	521	916	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	80.3956	477	916	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.4484	413	916	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.4419	405	916	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.2079	387	916	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.065	355	916	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	78.7525	307	916	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.4369	316	916	95	below_threshold
Tsuneonella suprasediminis	strain=Ery12	GCA_003605755.1	2306996	2306996	type	True	78.3263	329	916	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.3258	315	916	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	78.2296	254	916	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.1313	313	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:20,235] [INFO] DFAST Taxonomy check result was written to GCF_009827495.1_ASM982749v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:20,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:20,236] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:20,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f679f6b-67b7-4ce6-8816-b7c84c3055fb/dqc_reference/checkm_data
[2024-01-24 14:31:20,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:20,263] [INFO] Task started: CheckM
[2024-01-24 14:31:20,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827495.1_ASM982749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827495.1_ASM982749v1_genomic.fna/checkm_input GCF_009827495.1_ASM982749v1_genomic.fna/checkm_result
[2024-01-24 14:31:45,049] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:45,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:45,064] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:45,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:45,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827495.1_ASM982749v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:45,065] [INFO] Task started: Blastn
[2024-01-24 14:31:45,065] [INFO] Running command: blastn -query GCF_009827495.1_ASM982749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f679f6b-67b7-4ce6-8816-b7c84c3055fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827495.1_ASM982749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:46,389] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:46,392] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:46,392] [INFO] Target genome list was writen to GCF_009827495.1_ASM982749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:46,401] [INFO] Task started: fastANI
[2024-01-24 14:31:46,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg05e3a001-e7e6-41a7-b8e0-4c039a7723eb/GCF_009827495.1_ASM982749v1_genomic.fna.gz --refList GCF_009827495.1_ASM982749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827495.1_ASM982749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:59,200] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:59,211] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:59,212] [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_009827495.1	s__Tsuneonella aeria	100.0	916	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003958625.1	s__Tsuneonella rigui	81.0493	534	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	80.9679	529	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441535.1	s__Tsuneonella troitsensis	80.8558	521	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007065885.1	s__Tsuneonella sp007065885	80.8362	523	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698205.1	s__Tsuneonella dongtanensis	80.4139	469	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644315.1	s__Tsuneonella deserti	80.3956	477	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269345.1	s__Tsuneonella mangrovi	79.2996	392	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	79.108	343	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320115.1	s__Croceibacterium segetis	79.097	313	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.0469	357	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	78.8404	332	916	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	78.7668	306	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408095.1	s__Novosphingobium marinum	78.2947	273	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005884405.1	s__Qipengyuania marisflavi	78.2909	284	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605755.1	s__Tsuneonella suprasediminis	78.2893	333	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355455.1	s__Qipengyuania aurea	78.1567	299	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	78.1313	313	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:59,213] [INFO] GTDB search result was written to GCF_009827495.1_ASM982749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:59,213] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:59,217] [INFO] DFAST_QC result json was written to GCF_009827495.1_ASM982749v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:59,217] [INFO] DFAST_QC completed!
[2024-01-24 14:31:59,217] [INFO] Total running time: 0h0m59s