[2024-01-24 12:14:34,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,035] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,035] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c280684-fe5e-4e30-9bf3-484b75a9d519/dqc_reference
[2024-01-24 12:14:35,306] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,307] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,307] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd8e445b-0ba5-4b3f-b63c-aef8b0ba115f/GCF_018682675.1_ASM1868267v1_genomic.fna.gz | prodigal -d GCF_018682675.1_ASM1868267v1_genomic.fna/cds.fna -a GCF_018682675.1_ASM1868267v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:44,070] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:44,071] [INFO] Task started: HMMsearch
[2024-01-24 12:14:44,071] [INFO] Running command: hmmsearch --tblout GCF_018682675.1_ASM1868267v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c280684-fe5e-4e30-9bf3-484b75a9d519/dqc_reference/reference_markers.hmm GCF_018682675.1_ASM1868267v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:44,393] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:44,394] [INFO] Found 6/6 markers.
[2024-01-24 12:14:44,425] [INFO] Query marker FASTA was written to GCF_018682675.1_ASM1868267v1_genomic.fna/markers.fasta
[2024-01-24 12:14:44,425] [INFO] Task started: Blastn
[2024-01-24 12:14:44,425] [INFO] Running command: blastn -query GCF_018682675.1_ASM1868267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c280684-fe5e-4e30-9bf3-484b75a9d519/dqc_reference/reference_markers.fasta -out GCF_018682675.1_ASM1868267v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:45,409] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:45,412] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:45,412] [INFO] Target genome list was writen to GCF_018682675.1_ASM1868267v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:45,421] [INFO] Task started: fastANI
[2024-01-24 12:14:45,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd8e445b-0ba5-4b3f-b63c-aef8b0ba115f/GCF_018682675.1_ASM1868267v1_genomic.fna.gz --refList GCF_018682675.1_ASM1868267v1_genomic.fna/target_genomes.txt --output GCF_018682675.1_ASM1868267v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:00,295] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:00,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c280684-fe5e-4e30-9bf3-484b75a9d519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:00,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c280684-fe5e-4e30-9bf3-484b75a9d519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:00,306] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:00,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:00,307] [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
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	99.9999	1148	1156	95	conclusive
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	85.6376	809	1156	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	85.3738	812	1156	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	85.0793	847	1156	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	84.8729	815	1156	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	84.555	801	1156	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	84.5518	816	1156	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	84.4217	684	1156	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	84.4043	756	1156	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	84.355	746	1156	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	84.2964	759	1156	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	83.7158	727	1156	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.8012	291	1156	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.7781	263	1156	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.7366	367	1156	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.7067	253	1156	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.6751	232	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:00,308] [INFO] DFAST Taxonomy check result was written to GCF_018682675.1_ASM1868267v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:00,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:00,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:00,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c280684-fe5e-4e30-9bf3-484b75a9d519/dqc_reference/checkm_data
[2024-01-24 12:15:00,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:00,346] [INFO] Task started: CheckM
[2024-01-24 12:15:00,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018682675.1_ASM1868267v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018682675.1_ASM1868267v1_genomic.fna/checkm_input GCF_018682675.1_ASM1868267v1_genomic.fna/checkm_result
[2024-01-24 12:15:27,761] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:27,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:27,777] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:27,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:27,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018682675.1_ASM1868267v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:27,778] [INFO] Task started: Blastn
[2024-01-24 12:15:27,778] [INFO] Running command: blastn -query GCF_018682675.1_ASM1868267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c280684-fe5e-4e30-9bf3-484b75a9d519/dqc_reference/reference_markers_gtdb.fasta -out GCF_018682675.1_ASM1868267v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:29,592] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:29,594] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:29,595] [INFO] Target genome list was writen to GCF_018682675.1_ASM1868267v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:29,601] [INFO] Task started: fastANI
[2024-01-24 12:15:29,601] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd8e445b-0ba5-4b3f-b63c-aef8b0ba115f/GCF_018682675.1_ASM1868267v1_genomic.fna.gz --refList GCF_018682675.1_ASM1868267v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018682675.1_ASM1868267v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:43,276] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:43,285] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:43,286] [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_018682675.1	s__Sphingopyxis soli	99.9999	1148	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001468395.1	s__Sphingopyxis sp001468395	93.3711	981	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCF_001468265.1	s__Sphingopyxis sp001468265	87.1715	863	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463645.1	s__Sphingopyxis sp016463645	86.299	786	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821905.1	s__Sphingopyxis sp013821905	86.048	692	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795895.1	s__Sphingopyxis sp004795895	85.6688	863	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309275.1	s__Sphingopyxis sp017309275	85.6532	804	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	85.4504	821	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002277025.1	s__Sphingopyxis sp002277025	85.3955	832	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468285.1	s__Sphingopyxis sp001468285	85.3066	844	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000756375.1	s__Sphingopyxis sp000756375	85.2339	811	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873485.1	s__Sphingopyxis sp014873485	85.0475	814	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	84.9396	801	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCA_016793775.1	s__Sphingopyxis sp016793775	84.6822	786	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:43,287] [INFO] GTDB search result was written to GCF_018682675.1_ASM1868267v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:43,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:43,291] [INFO] DFAST_QC result json was written to GCF_018682675.1_ASM1868267v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:43,291] [INFO] DFAST_QC completed!
[2024-01-24 12:15:43,291] [INFO] Total running time: 0h1m9s