[2024-01-25 17:44:20,659] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:20,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:20,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg221a4d0d-a812-43ba-a0bb-dfac22fec758/dqc_reference
[2024-01-25 17:44:21,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:21,774] [INFO] Task started: Prodigal
[2024-01-25 17:44:21,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg3aa526b4-b5ab-4941-89e9-0362946439e6/GCF_014395975.1_ASM1439597v1_genomic.fna.gz | prodigal -d GCF_014395975.1_ASM1439597v1_genomic.fna/cds.fna -a GCF_014395975.1_ASM1439597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:37,808] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:37,808] [INFO] Task started: HMMsearch
[2024-01-25 17:44:37,808] [INFO] Running command: hmmsearch --tblout GCF_014395975.1_ASM1439597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg221a4d0d-a812-43ba-a0bb-dfac22fec758/dqc_reference/reference_markers.hmm GCF_014395975.1_ASM1439597v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:38,086] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:38,087] [INFO] Found 6/6 markers.
[2024-01-25 17:44:38,131] [INFO] Query marker FASTA was written to GCF_014395975.1_ASM1439597v1_genomic.fna/markers.fasta
[2024-01-25 17:44:38,131] [INFO] Task started: Blastn
[2024-01-25 17:44:38,131] [INFO] Running command: blastn -query GCF_014395975.1_ASM1439597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg221a4d0d-a812-43ba-a0bb-dfac22fec758/dqc_reference/reference_markers.fasta -out GCF_014395975.1_ASM1439597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:39,042] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:39,044] [INFO] Selected 16 target genomes.
[2024-01-25 17:44:39,045] [INFO] Target genome list was writen to GCF_014395975.1_ASM1439597v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:39,057] [INFO] Task started: fastANI
[2024-01-25 17:44:39,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aa526b4-b5ab-4941-89e9-0362946439e6/GCF_014395975.1_ASM1439597v1_genomic.fna.gz --refList GCF_014395975.1_ASM1439597v1_genomic.fna/target_genomes.txt --output GCF_014395975.1_ASM1439597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:54,010] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:54,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg221a4d0d-a812-43ba-a0bb-dfac22fec758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:54,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg221a4d0d-a812-43ba-a0bb-dfac22fec758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:54,021] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:54,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:54,021] [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
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	100.0	1720	1722	95	conclusive
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	83.9239	1117	1722	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	82.831	981	1722	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.2715	768	1722	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.2262	679	1722	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.3782	393	1722	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	80.2802	582	1722	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	80.2661	604	1722	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	80.2469	568	1722	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	80.1753	603	1722	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	80.1536	694	1722	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	80.0422	604	1722	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.8464	625	1722	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.7061	556	1722	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.3904	484	1722	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.0627	572	1722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:54,023] [INFO] DFAST Taxonomy check result was written to GCF_014395975.1_ASM1439597v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:54,024] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:54,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:54,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg221a4d0d-a812-43ba-a0bb-dfac22fec758/dqc_reference/checkm_data
[2024-01-25 17:44:54,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:54,073] [INFO] Task started: CheckM
[2024-01-25 17:44:54,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014395975.1_ASM1439597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014395975.1_ASM1439597v1_genomic.fna/checkm_input GCF_014395975.1_ASM1439597v1_genomic.fna/checkm_result
[2024-01-25 17:47:33,521] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:33,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:33,552] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:33,552] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:33,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014395975.1_ASM1439597v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:33,554] [INFO] Task started: Blastn
[2024-01-25 17:47:33,554] [INFO] Running command: blastn -query GCF_014395975.1_ASM1439597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg221a4d0d-a812-43ba-a0bb-dfac22fec758/dqc_reference/reference_markers_gtdb.fasta -out GCF_014395975.1_ASM1439597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:35,553] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:35,557] [INFO] Selected 8 target genomes.
[2024-01-25 17:47:35,557] [INFO] Target genome list was writen to GCF_014395975.1_ASM1439597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:35,568] [INFO] Task started: fastANI
[2024-01-25 17:47:35,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aa526b4-b5ab-4941-89e9-0362946439e6/GCF_014395975.1_ASM1439597v1_genomic.fna.gz --refList GCF_014395975.1_ASM1439597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014395975.1_ASM1439597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:46,015] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:46,021] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:46,022] [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_014395975.1	s__Diaphorobacter_A ruginosibacter	100.0	1720	1722	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015354245.1	s__Diaphorobacter_A sp015354245	83.9091	1118	1722	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011305535.1	s__Diaphorobacter_A sp011305535	83.4842	1120	1722	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011305995.1	s__Diaphorobacter_A sp011305995	82.8653	1135	1722	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489535.1	s__Diaphorobacter_A aerolatus	82.8317	981	1722	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331385.1	s__Diaphorobacter_A sp002331385	81.9284	897	1722	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter_A	95.0	95.84	95.84	0.86	0.86	2	-
GCF_001544075.1	s__Comamonas terrae	81.2767	768	1722	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424265.1	s__Acidovorax_A sp001424265	80.9957	714	1722	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:46,023] [INFO] GTDB search result was written to GCF_014395975.1_ASM1439597v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:46,023] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:46,026] [INFO] DFAST_QC result json was written to GCF_014395975.1_ASM1439597v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:46,026] [INFO] DFAST_QC completed!
[2024-01-25 17:47:46,026] [INFO] Total running time: 0h3m25s