[2024-01-24 13:31:31,660] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:31,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:31,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a38890a-bb8f-44b7-8637-b2ca59fab2bc/dqc_reference
[2024-01-24 13:31:32,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:32,882] [INFO] Task started: Prodigal
[2024-01-24 13:31:32,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c7d5667-ebde-4991-a0a4-e980e71610e1/GCF_016907975.1_ASM1690797v1_genomic.fna.gz | prodigal -d GCF_016907975.1_ASM1690797v1_genomic.fna/cds.fna -a GCF_016907975.1_ASM1690797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:43,813] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:43,813] [INFO] Task started: HMMsearch
[2024-01-24 13:31:43,813] [INFO] Running command: hmmsearch --tblout GCF_016907975.1_ASM1690797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a38890a-bb8f-44b7-8637-b2ca59fab2bc/dqc_reference/reference_markers.hmm GCF_016907975.1_ASM1690797v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:44,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:44,129] [INFO] Found 6/6 markers.
[2024-01-24 13:31:44,201] [INFO] Query marker FASTA was written to GCF_016907975.1_ASM1690797v1_genomic.fna/markers.fasta
[2024-01-24 13:31:44,202] [INFO] Task started: Blastn
[2024-01-24 13:31:44,202] [INFO] Running command: blastn -query GCF_016907975.1_ASM1690797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a38890a-bb8f-44b7-8637-b2ca59fab2bc/dqc_reference/reference_markers.fasta -out GCF_016907975.1_ASM1690797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:45,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:45,371] [INFO] Selected 25 target genomes.
[2024-01-24 13:31:45,371] [INFO] Target genome list was writen to GCF_016907975.1_ASM1690797v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:45,396] [INFO] Task started: fastANI
[2024-01-24 13:31:45,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c7d5667-ebde-4991-a0a4-e980e71610e1/GCF_016907975.1_ASM1690797v1_genomic.fna.gz --refList GCF_016907975.1_ASM1690797v1_genomic.fna/target_genomes.txt --output GCF_016907975.1_ASM1690797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:12,236] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:12,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a38890a-bb8f-44b7-8637-b2ca59fab2bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:12,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a38890a-bb8f-44b7-8637-b2ca59fab2bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:12,257] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:12,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:12,257] [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
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	81.0797	719	1373	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.4376	477	1373	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.3613	518	1373	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	78.2116	486	1373	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	78.2012	480	1373	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	78.1343	356	1373	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	78.0905	505	1373	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.076	573	1373	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	78.032	440	1373	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	77.9814	452	1373	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.8469	547	1373	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	77.7513	379	1373	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	77.6911	356	1373	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.6594	406	1373	95	below_threshold
Chelatococcus reniformis	strain=CGMCC 1.12919	GCA_014640075.1	1494448	1494448	type	True	77.6592	397	1373	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.6322	522	1373	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.6131	551	1373	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.6101	420	1373	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.559	476	1373	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.522	421	1373	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.519	425	1373	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	77.4832	518	1373	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.4581	548	1373	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	77.3032	411	1373	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	77.156	402	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:12,261] [INFO] DFAST Taxonomy check result was written to GCF_016907975.1_ASM1690797v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:12,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:12,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:12,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a38890a-bb8f-44b7-8637-b2ca59fab2bc/dqc_reference/checkm_data
[2024-01-24 13:32:12,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:12,313] [INFO] Task started: CheckM
[2024-01-24 13:32:12,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907975.1_ASM1690797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907975.1_ASM1690797v1_genomic.fna/checkm_input GCF_016907975.1_ASM1690797v1_genomic.fna/checkm_result
[2024-01-24 13:32:47,613] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:47,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:47,628] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:47,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:47,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907975.1_ASM1690797v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:47,629] [INFO] Task started: Blastn
[2024-01-24 13:32:47,629] [INFO] Running command: blastn -query GCF_016907975.1_ASM1690797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a38890a-bb8f-44b7-8637-b2ca59fab2bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907975.1_ASM1690797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:49,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:49,812] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:49,812] [INFO] Target genome list was writen to GCF_016907975.1_ASM1690797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:49,818] [INFO] Task started: fastANI
[2024-01-24 13:32:49,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c7d5667-ebde-4991-a0a4-e980e71610e1/GCF_016907975.1_ASM1690797v1_genomic.fna.gz --refList GCF_016907975.1_ASM1690797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907975.1_ASM1690797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:57,742] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:57,749] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:57,749] [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_016907975.1	s__Methylopila capsulata	100.0	1373	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000526315.1	s__Methylopila sp000526315	93.5105	1204	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897035.1	s__Methylopila sp002897035	91.4981	1186	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241695.1	s__Hansschlegelia sp003241695	81.3401	808	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168115.1	s__Hansschlegelia sp902168115	81.2461	775	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	81.1442	798	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196425.1	s__Hansschlegelia beijingensis	81.1011	717	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:57,751] [INFO] GTDB search result was written to GCF_016907975.1_ASM1690797v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:57,751] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:57,755] [INFO] DFAST_QC result json was written to GCF_016907975.1_ASM1690797v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:57,755] [INFO] DFAST_QC completed!
[2024-01-24 13:32:57,755] [INFO] Total running time: 0h1m26s