[2024-01-24 12:36:24,567] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,570] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc12e6c5-966c-416b-88de-0e71ae1d3bf9/dqc_reference
[2024-01-24 12:36:25,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,957] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,957] [INFO] Running command: gunzip -c /var/lib/cwl/stgea5f2b6f-9a55-4414-b99d-816205ce9f67/GCF_014645195.1_ASM1464519v1_genomic.fna.gz | prodigal -d GCF_014645195.1_ASM1464519v1_genomic.fna/cds.fna -a GCF_014645195.1_ASM1464519v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:40,535] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:40,535] [INFO] Task started: HMMsearch
[2024-01-24 12:36:40,536] [INFO] Running command: hmmsearch --tblout GCF_014645195.1_ASM1464519v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc12e6c5-966c-416b-88de-0e71ae1d3bf9/dqc_reference/reference_markers.hmm GCF_014645195.1_ASM1464519v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:40,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:40,834] [INFO] Found 6/6 markers.
[2024-01-24 12:36:40,878] [INFO] Query marker FASTA was written to GCF_014645195.1_ASM1464519v1_genomic.fna/markers.fasta
[2024-01-24 12:36:40,878] [INFO] Task started: Blastn
[2024-01-24 12:36:40,878] [INFO] Running command: blastn -query GCF_014645195.1_ASM1464519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc12e6c5-966c-416b-88de-0e71ae1d3bf9/dqc_reference/reference_markers.fasta -out GCF_014645195.1_ASM1464519v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:41,901] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:41,906] [INFO] Selected 15 target genomes.
[2024-01-24 12:36:41,907] [INFO] Target genome list was writen to GCF_014645195.1_ASM1464519v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:41,915] [INFO] Task started: fastANI
[2024-01-24 12:36:41,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgea5f2b6f-9a55-4414-b99d-816205ce9f67/GCF_014645195.1_ASM1464519v1_genomic.fna.gz --refList GCF_014645195.1_ASM1464519v1_genomic.fna/target_genomes.txt --output GCF_014645195.1_ASM1464519v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:56,940] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:56,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc12e6c5-966c-416b-88de-0e71ae1d3bf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:56,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc12e6c5-966c-416b-88de-0e71ae1d3bf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:56,958] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:56,958] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:56,958] [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
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	100.0	1605	1607	95	conclusive
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	86.6353	1019	1607	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	83.8272	863	1607	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	81.9108	716	1607	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	81.8091	695	1607	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	81.492	668	1607	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	81.1578	658	1607	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	80.8263	647	1607	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	80.6874	697	1607	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.6244	636	1607	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	80.5111	604	1607	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.4762	647	1607	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.8247	546	1607	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.5391	460	1607	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.2987	493	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:56,960] [INFO] DFAST Taxonomy check result was written to GCF_014645195.1_ASM1464519v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:56,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:56,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:56,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc12e6c5-966c-416b-88de-0e71ae1d3bf9/dqc_reference/checkm_data
[2024-01-24 12:36:56,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:57,017] [INFO] Task started: CheckM
[2024-01-24 12:36:57,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645195.1_ASM1464519v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645195.1_ASM1464519v1_genomic.fna/checkm_input GCF_014645195.1_ASM1464519v1_genomic.fna/checkm_result
[2024-01-24 12:37:40,413] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:40,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:40,434] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:40,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:40,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645195.1_ASM1464519v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:40,435] [INFO] Task started: Blastn
[2024-01-24 12:37:40,435] [INFO] Running command: blastn -query GCF_014645195.1_ASM1464519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc12e6c5-966c-416b-88de-0e71ae1d3bf9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645195.1_ASM1464519v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:42,344] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:42,348] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:42,348] [INFO] Target genome list was writen to GCF_014645195.1_ASM1464519v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:42,363] [INFO] Task started: fastANI
[2024-01-24 12:37:42,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgea5f2b6f-9a55-4414-b99d-816205ce9f67/GCF_014645195.1_ASM1464519v1_genomic.fna.gz --refList GCF_014645195.1_ASM1464519v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645195.1_ASM1464519v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:56,644] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:56,659] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:56,659] [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_014645195.1	s__Novosphingobium indicum	100.0	1605	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	conclusive
GCF_000802225.1	s__Novosphingobium malaysiense	86.6526	1017	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	83.822	864	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	82.6802	799	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	81.9145	716	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_900168325.1	s__Novosphingobium mathurense	81.5028	667	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_900113255.1	s__Novosphingobium sp900113255	81.4287	685	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874585.1	s__Novosphingobium sp006874585	81.3751	709	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_000281975.1	s__Novosphingobium sp000281975	80.9805	712	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341845.1	s__Novosphingobium sp004341845	80.9503	672	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015865035.1	s__Novosphingobium sp015865035	80.8263	647	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018417475.1	s__Novosphingobium sp000813185	80.6307	636	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_009856825.1	s__Novosphingobium sp009856825	80.5111	604	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	80.486	646	1607	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 12:37:56,664] [INFO] GTDB search result was written to GCF_014645195.1_ASM1464519v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:56,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:56,668] [INFO] DFAST_QC result json was written to GCF_014645195.1_ASM1464519v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:56,669] [INFO] DFAST_QC completed!
[2024-01-24 12:37:56,669] [INFO] Total running time: 0h1m32s