[2024-01-24 12:40:20,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,073] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,074] [INFO] DQC Reference Directory: /var/lib/cwl/stgb34997bd-a058-47c6-8607-5c32c939ba72/dqc_reference
[2024-01-24 12:40:21,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:21,310] [INFO] Task started: Prodigal
[2024-01-24 12:40:21,311] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0f0e785-4300-4417-bfc4-eb18d8f809da/GCF_018982885.2_ASM1898288v2_genomic.fna.gz | prodigal -d GCF_018982885.2_ASM1898288v2_genomic.fna/cds.fna -a GCF_018982885.2_ASM1898288v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:35,289] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:35,290] [INFO] Task started: HMMsearch
[2024-01-24 12:40:35,290] [INFO] Running command: hmmsearch --tblout GCF_018982885.2_ASM1898288v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb34997bd-a058-47c6-8607-5c32c939ba72/dqc_reference/reference_markers.hmm GCF_018982885.2_ASM1898288v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:35,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:35,559] [INFO] Found 6/6 markers.
[2024-01-24 12:40:35,601] [INFO] Query marker FASTA was written to GCF_018982885.2_ASM1898288v2_genomic.fna/markers.fasta
[2024-01-24 12:40:35,601] [INFO] Task started: Blastn
[2024-01-24 12:40:35,601] [INFO] Running command: blastn -query GCF_018982885.2_ASM1898288v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34997bd-a058-47c6-8607-5c32c939ba72/dqc_reference/reference_markers.fasta -out GCF_018982885.2_ASM1898288v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:36,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:36,508] [INFO] Selected 26 target genomes.
[2024-01-24 12:40:36,508] [INFO] Target genome list was writen to GCF_018982885.2_ASM1898288v2_genomic.fna/target_genomes.txt
[2024-01-24 12:40:36,541] [INFO] Task started: fastANI
[2024-01-24 12:40:36,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0f0e785-4300-4417-bfc4-eb18d8f809da/GCF_018982885.2_ASM1898288v2_genomic.fna.gz --refList GCF_018982885.2_ASM1898288v2_genomic.fna/target_genomes.txt --output GCF_018982885.2_ASM1898288v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:52,849] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:52,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb34997bd-a058-47c6-8607-5c32c939ba72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:52,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb34997bd-a058-47c6-8607-5c32c939ba72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:52,872] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:52,872] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:52,873] [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
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	78.0414	380	1630	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009372075.1	1439888	1439888	type	True	78.0224	382	1630	95	below_threshold
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	77.9567	393	1630	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	77.9001	371	1630	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	77.7768	278	1630	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	77.7312	300	1630	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	77.5	389	1630	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	77.2937	238	1630	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.285	372	1630	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	77.2619	274	1630	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	77.2468	361	1630	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	77.2365	356	1630	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.189	409	1630	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.1827	407	1630	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	77.152	288	1630	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	77.1186	331	1630	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.0508	240	1630	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	76.9658	195	1630	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.9517	307	1630	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	76.9413	295	1630	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	76.9047	285	1630	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	76.8306	220	1630	95	below_threshold
Sphingopyxis flava	strain=R11H	GCA_900168005.1	1507287	1507287	type	True	76.5706	187	1630	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	76.1168	97	1630	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	76.0375	131	1630	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	75.8239	140	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:52,874] [INFO] DFAST Taxonomy check result was written to GCF_018982885.2_ASM1898288v2_genomic.fna/tc_result.tsv
[2024-01-24 12:40:52,875] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:52,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:52,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb34997bd-a058-47c6-8607-5c32c939ba72/dqc_reference/checkm_data
[2024-01-24 12:40:52,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:52,921] [INFO] Task started: CheckM
[2024-01-24 12:40:52,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018982885.2_ASM1898288v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018982885.2_ASM1898288v2_genomic.fna/checkm_input GCF_018982885.2_ASM1898288v2_genomic.fna/checkm_result
[2024-01-24 12:41:34,337] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:34,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:34,358] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:34,358] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:34,358] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018982885.2_ASM1898288v2_genomic.fna/markers.fasta)
[2024-01-24 12:41:34,359] [INFO] Task started: Blastn
[2024-01-24 12:41:34,359] [INFO] Running command: blastn -query GCF_018982885.2_ASM1898288v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34997bd-a058-47c6-8607-5c32c939ba72/dqc_reference/reference_markers_gtdb.fasta -out GCF_018982885.2_ASM1898288v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:36,017] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:36,021] [INFO] Selected 11 target genomes.
[2024-01-24 12:41:36,021] [INFO] Target genome list was writen to GCF_018982885.2_ASM1898288v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:36,030] [INFO] Task started: fastANI
[2024-01-24 12:41:36,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0f0e785-4300-4417-bfc4-eb18d8f809da/GCF_018982885.2_ASM1898288v2_genomic.fna.gz --refList GCF_018982885.2_ASM1898288v2_genomic.fna/target_genomes_gtdb.txt --output GCF_018982885.2_ASM1898288v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:44,965] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:44,981] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:44,982] [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_018982885.1	s__CAHJWT01 sp018982885	99.9627	1562	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903643075.1	s__CAHJWT01 sp903643075	82.4958	451	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642255.1	s__CAHJWT01 sp903642255	82.2995	447	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019245455.1	s__CAHJWT01 sp019245455	81.0632	496	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018982925.1	s__Glacieibacterium sp018982925	80.1464	622	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097155.1	s__Glacieibacterium frigidum	79.8322	566	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	78.8349	385	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241875.1	s__Polymorphobacter sp003241875	78.0841	424	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643455.1	s__Polymorphobacter glacialis	77.8917	372	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	77.0721	372	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_019075875.1	s__Novosphingobium sp019075875	77.0015	274	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:44,983] [INFO] GTDB search result was written to GCF_018982885.2_ASM1898288v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:44,983] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:44,987] [INFO] DFAST_QC result json was written to GCF_018982885.2_ASM1898288v2_genomic.fna/dqc_result.json
[2024-01-24 12:41:44,987] [INFO] DFAST_QC completed!
[2024-01-24 12:41:44,988] [INFO] Total running time: 0h1m25s