[2023-06-28 11:10:19,785] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:10:19,787] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:10:19,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg23fecb5f-2d54-4a31-9a4c-c2c63d077f59/dqc_reference
[2023-06-28 11:10:20,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:10:20,994] [INFO] Task started: Prodigal
[2023-06-28 11:10:20,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg4909a28a-81bb-4af1-9103-a7fa0ab1108e/GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna.gz | prodigal -d GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/cds.fna -a GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:10:28,820] [INFO] Task succeeded: Prodigal
[2023-06-28 11:10:28,821] [INFO] Task started: HMMsearch
[2023-06-28 11:10:28,821] [INFO] Running command: hmmsearch --tblout GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23fecb5f-2d54-4a31-9a4c-c2c63d077f59/dqc_reference/reference_markers.hmm GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:10:29,065] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:10:29,066] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4909a28a-81bb-4af1-9103-a7fa0ab1108e/GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna.gz]
[2023-06-28 11:10:29,097] [INFO] Query marker FASTA was written to GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/markers.fasta
[2023-06-28 11:10:29,097] [INFO] Task started: Blastn
[2023-06-28 11:10:29,097] [INFO] Running command: blastn -query GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/markers.fasta -db /var/lib/cwl/stg23fecb5f-2d54-4a31-9a4c-c2c63d077f59/dqc_reference/reference_markers.fasta -out GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:10:30,067] [INFO] Task succeeded: Blastn
[2023-06-28 11:10:30,075] [INFO] Selected 17 target genomes.
[2023-06-28 11:10:30,076] [INFO] Target genome list was writen to GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/target_genomes.txt
[2023-06-28 11:10:30,080] [INFO] Task started: fastANI
[2023-06-28 11:10:30,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg4909a28a-81bb-4af1-9103-a7fa0ab1108e/GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna.gz --refList GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/target_genomes.txt --output GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:10:44,059] [INFO] Task succeeded: fastANI
[2023-06-28 11:10:44,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23fecb5f-2d54-4a31-9a4c-c2c63d077f59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:10:44,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23fecb5f-2d54-4a31-9a4c-c2c63d077f59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:10:44,079] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2023-06-28 11:10:44,079] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-28 11:10:44,080] [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
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	95.6441	727	879	95	inconclusive
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	95.5944	747	879	95	inconclusive
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	95.5025	671	879	95	inconclusive
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	83.9071	588	879	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	83.3625	564	879	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	81.1754	505	879	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	80.8804	467	879	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	80.8663	467	879	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	80.5974	482	879	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	80.4533	469	879	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	80.3498	475	879	95	below_threshold
Sphingomonas albertensis	strain=DOAB 1063	GCA_014358075.1	2762591	2762591	type	True	79.7377	411	879	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.7232	475	879	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.7009	476	879	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.5911	411	879	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.4255	429	879	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.4172	418	879	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:10:44,083] [INFO] DFAST Taxonomy check result was written to GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/tc_result.tsv
[2023-06-28 11:10:44,084] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:10:44,084] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:10:44,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23fecb5f-2d54-4a31-9a4c-c2c63d077f59/dqc_reference/checkm_data
[2023-06-28 11:10:44,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:10:44,125] [INFO] Task started: CheckM
[2023-06-28 11:10:44,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/checkm_input GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/checkm_result
[2023-06-28 11:11:11,872] [INFO] Task succeeded: CheckM
[2023-06-28 11:11:11,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.72%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 11:11:11,897] [INFO] ===== Completeness check finished =====
[2023-06-28 11:11:11,898] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:11:11,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/markers.fasta)
[2023-06-28 11:11:11,898] [INFO] Task started: Blastn
[2023-06-28 11:11:11,899] [INFO] Running command: blastn -query GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/markers.fasta -db /var/lib/cwl/stg23fecb5f-2d54-4a31-9a4c-c2c63d077f59/dqc_reference/reference_markers_gtdb.fasta -out GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:11:13,714] [INFO] Task succeeded: Blastn
[2023-06-28 11:11:13,732] [INFO] Selected 15 target genomes.
[2023-06-28 11:11:13,732] [INFO] Target genome list was writen to GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:11:13,770] [INFO] Task started: fastANI
[2023-06-28 11:11:13,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg4909a28a-81bb-4af1-9103-a7fa0ab1108e/GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna.gz --refList GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/target_genomes_gtdb.txt --output GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:11:26,059] [INFO] Task succeeded: fastANI
[2023-06-28 11:11:26,078] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:11:26,078] [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_014196115.1	s__Sphingomonas aquatilis	95.6441	727	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	conclusive
GCA_003075315.1	s__Sphingomonas sp003075315	93.2357	728	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCA_002292295.1	s__Sphingomonas sp002292295	84.3935	576	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	83.962	590	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	83.8866	589	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_010450875.1	s__Sphingomonas insulae	83.3656	564	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003355005.1	s__Sphingomonas sp003355005	82.9823	565	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107325.1	s__Sphingomonas sp016107325	82.4472	560	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197105.1	s__Sphingomonas jinjuensis	81.2199	502	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	80.8497	454	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	80.8204	471	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_019112965.1	s__Sphingomonas excrementigallinarum	80.7157	442	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	80.628	440	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	80.5621	486	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340945.1	s__Sphingomonas sp004340945	79.6832	457	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-28 11:11:26,080] [INFO] GTDB search result was written to GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/result_gtdb.tsv
[2023-06-28 11:11:26,081] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:11:26,084] [INFO] DFAST_QC result json was written to GCA_913773775.1_SP223_1_metabat2_genome_mining.22_cleaned_genomic.fna/dqc_result.json
[2023-06-28 11:11:26,085] [INFO] DFAST_QC completed!
[2023-06-28 11:11:26,085] [INFO] Total running time: 0h1m6s