[2024-01-24 13:28:13,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dbfc4c0-3697-4e13-a148-25fe83807fad/dqc_reference
[2024-01-24 13:28:14,391] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,391] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,392] [INFO] Running command: gunzip -c /var/lib/cwl/stg4549133f-b101-4ace-82e6-bba5ec6f2138/GCF_000176855.2_ASM17685v2_genomic.fna.gz | prodigal -d GCF_000176855.2_ASM17685v2_genomic.fna/cds.fna -a GCF_000176855.2_ASM17685v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:34,294] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:34,294] [INFO] Task started: HMMsearch
[2024-01-24 13:28:34,294] [INFO] Running command: hmmsearch --tblout GCF_000176855.2_ASM17685v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dbfc4c0-3697-4e13-a148-25fe83807fad/dqc_reference/reference_markers.hmm GCF_000176855.2_ASM17685v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:34,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:34,690] [INFO] Found 6/6 markers.
[2024-01-24 13:28:34,754] [INFO] Query marker FASTA was written to GCF_000176855.2_ASM17685v2_genomic.fna/markers.fasta
[2024-01-24 13:28:34,754] [INFO] Task started: Blastn
[2024-01-24 13:28:34,754] [INFO] Running command: blastn -query GCF_000176855.2_ASM17685v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dbfc4c0-3697-4e13-a148-25fe83807fad/dqc_reference/reference_markers.fasta -out GCF_000176855.2_ASM17685v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:35,900] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:35,903] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:35,904] [INFO] Target genome list was writen to GCF_000176855.2_ASM17685v2_genomic.fna/target_genomes.txt
[2024-01-24 13:28:35,913] [INFO] Task started: fastANI
[2024-01-24 13:28:35,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg4549133f-b101-4ace-82e6-bba5ec6f2138/GCF_000176855.2_ASM17685v2_genomic.fna.gz --refList GCF_000176855.2_ASM17685v2_genomic.fna/target_genomes.txt --output GCF_000176855.2_ASM17685v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:54,322] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:54,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dbfc4c0-3697-4e13-a148-25fe83807fad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:54,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dbfc4c0-3697-4e13-a148-25fe83807fad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:54,340] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:54,340] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:28:54,341] [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
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	100.0	1827	1827	95	inconclusive
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	95.2137	1597	1827	95	inconclusive
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	93.1926	1425	1827	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	93.1436	1540	1827	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	85.8098	1256	1827	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	85.8057	1217	1827	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	84.9783	1121	1827	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	80.9519	881	1827	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.8451	830	1827	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.5987	678	1827	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.4297	695	1827	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.2858	676	1827	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.1499	750	1827	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:54,344] [INFO] DFAST Taxonomy check result was written to GCF_000176855.2_ASM17685v2_genomic.fna/tc_result.tsv
[2024-01-24 13:28:54,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:54,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:54,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dbfc4c0-3697-4e13-a148-25fe83807fad/dqc_reference/checkm_data
[2024-01-24 13:28:54,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:54,404] [INFO] Task started: CheckM
[2024-01-24 13:28:54,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000176855.2_ASM17685v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000176855.2_ASM17685v2_genomic.fna/checkm_input GCF_000176855.2_ASM17685v2_genomic.fna/checkm_result
[2024-01-24 13:30:44,865] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:44,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:44,886] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:44,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:44,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000176855.2_ASM17685v2_genomic.fna/markers.fasta)
[2024-01-24 13:30:44,887] [INFO] Task started: Blastn
[2024-01-24 13:30:44,887] [INFO] Running command: blastn -query GCF_000176855.2_ASM17685v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dbfc4c0-3697-4e13-a148-25fe83807fad/dqc_reference/reference_markers_gtdb.fasta -out GCF_000176855.2_ASM17685v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:47,036] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:47,039] [INFO] Selected 5 target genomes.
[2024-01-24 13:30:47,039] [INFO] Target genome list was writen to GCF_000176855.2_ASM17685v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:47,062] [INFO] Task started: fastANI
[2024-01-24 13:30:47,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg4549133f-b101-4ace-82e6-bba5ec6f2138/GCF_000176855.2_ASM17685v2_genomic.fna.gz --refList GCF_000176855.2_ASM17685v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000176855.2_ASM17685v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:55,335] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:55,346] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:55,347] [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_000176855.2	s__Acidovorax_A avenae	100.0	1827	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	conclusive
GCF_000687165.1	s__Acidovorax_A oryzae	95.2007	1598	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	98.08	98.08	0.87	0.87	2	-
GCF_900100305.1	s__Acidovorax_A citrulli	93.1998	1424	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCF_900104515.1	s__Acidovorax_A cattleyae	93.1739	1537	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.69	99.69	0.82	0.82	2	-
GCA_002397315.1	s__Acidovorax_A sp002397315	88.8654	1323	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:55,349] [INFO] GTDB search result was written to GCF_000176855.2_ASM17685v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:55,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:55,354] [INFO] DFAST_QC result json was written to GCF_000176855.2_ASM17685v2_genomic.fna/dqc_result.json
[2024-01-24 13:30:55,354] [INFO] DFAST_QC completed!
[2024-01-24 13:30:55,354] [INFO] Total running time: 0h2m42s