[2024-01-24 13:21:10,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:10,946] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:10,947] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeceacf3-93ea-451f-b569-a0fa45e33531/dqc_reference
[2024-01-24 13:21:12,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,155] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,155] [INFO] Running command: gunzip -c /var/lib/cwl/stg215ab818-7ff9-470e-a6ec-01c4c7cc1def/GCF_000017405.1_ASM1740v1_genomic.fna.gz | prodigal -d GCF_000017405.1_ASM1740v1_genomic.fna/cds.fna -a GCF_000017405.1_ASM1740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:28,053] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:28,054] [INFO] Task started: HMMsearch
[2024-01-24 13:21:28,054] [INFO] Running command: hmmsearch --tblout GCF_000017405.1_ASM1740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeceacf3-93ea-451f-b569-a0fa45e33531/dqc_reference/reference_markers.hmm GCF_000017405.1_ASM1740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:28,359] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:28,361] [INFO] Found 6/6 markers.
[2024-01-24 13:21:28,410] [INFO] Query marker FASTA was written to GCF_000017405.1_ASM1740v1_genomic.fna/markers.fasta
[2024-01-24 13:21:28,411] [INFO] Task started: Blastn
[2024-01-24 13:21:28,411] [INFO] Running command: blastn -query GCF_000017405.1_ASM1740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeceacf3-93ea-451f-b569-a0fa45e33531/dqc_reference/reference_markers.fasta -out GCF_000017405.1_ASM1740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:29,139] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:29,143] [INFO] Selected 12 target genomes.
[2024-01-24 13:21:29,144] [INFO] Target genome list was writen to GCF_000017405.1_ASM1740v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:29,159] [INFO] Task started: fastANI
[2024-01-24 13:21:29,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg215ab818-7ff9-470e-a6ec-01c4c7cc1def/GCF_000017405.1_ASM1740v1_genomic.fna.gz --refList GCF_000017405.1_ASM1740v1_genomic.fna/target_genomes.txt --output GCF_000017405.1_ASM1740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:41,579] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:41,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeceacf3-93ea-451f-b569-a0fa45e33531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:41,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeceacf3-93ea-451f-b569-a0fa45e33531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:41,591] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:21:41,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:41,591] [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
Brucella anthropi	strain=ATCC 49188	GCA_000017405.1	529	529	type	True	100.0	1729	1732	95	conclusive
Brucella anthropi	strain=NCTC12168	GCA_900454235.1	529	529	type	True	99.9929	1726	1732	95	conclusive
Brucella tritici	strain=LMG 18957	GCA_008932295.1	94626	94626	type	True	91.5998	1334	1732	95	below_threshold
Brucella pecoris	strain=DSM 23868	GCA_014197065.1	867683	867683	type	True	89.1961	1363	1732	95	below_threshold
Brucella pecoris	strain=08RB2639	GCA_006376675.1	867683	867683	type	True	89.1794	1356	1732	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	87.9711	1231	1732	95	below_threshold
Brucella intermedia	strain=LMG 3301	GCA_000182645.1	94625	94625	suspected-type	True	87.9581	1232	1732	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.9265	311	1732	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.8139	308	1732	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.182	292	1732	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.1145	221	1732	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	76.9802	208	1732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:41,594] [INFO] DFAST Taxonomy check result was written to GCF_000017405.1_ASM1740v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:41,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:41,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:41,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeceacf3-93ea-451f-b569-a0fa45e33531/dqc_reference/checkm_data
[2024-01-24 13:21:41,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:41,643] [INFO] Task started: CheckM
[2024-01-24 13:21:41,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000017405.1_ASM1740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000017405.1_ASM1740v1_genomic.fna/checkm_input GCF_000017405.1_ASM1740v1_genomic.fna/checkm_result
[2024-01-24 13:22:32,126] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:32,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:32,148] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:32,148] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:32,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000017405.1_ASM1740v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:32,149] [INFO] Task started: Blastn
[2024-01-24 13:22:32,149] [INFO] Running command: blastn -query GCF_000017405.1_ASM1740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeceacf3-93ea-451f-b569-a0fa45e33531/dqc_reference/reference_markers_gtdb.fasta -out GCF_000017405.1_ASM1740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:33,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:33,425] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:33,425] [INFO] Target genome list was writen to GCF_000017405.1_ASM1740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:33,428] [INFO] Task started: fastANI
[2024-01-24 13:22:33,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg215ab818-7ff9-470e-a6ec-01c4c7cc1def/GCF_000017405.1_ASM1740v1_genomic.fna.gz --refList GCF_000017405.1_ASM1740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000017405.1_ASM1740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:48,392] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:48,410] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:48,410] [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_000017405.1	s__Ochrobactrum anthropi	100.0	1729	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.518	98.11	96.94	0.89	0.83	55	conclusive
GCA_012103075.1	s__Ochrobactrum cytisi	95.515	1372	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.518	98.45	98.45	0.94	0.94	2	-
GCF_008932295.1	s__Ochrobactrum tritici	91.6205	1332	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	98.18	96.73	0.91	0.84	6	-
GCF_902825325.1	s__Ochrobactrum sp003176975	90.8806	1306	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.64	97.64	0.88	0.88	2	-
GCA_012103035.1	s__Ochrobactrum oryzae	89.3372	1234	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.03	98.38	0.88	0.83	3	-
GCF_006376675.1	s__Ochrobactrum pecoris	89.1794	1356	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.97	99.94	1.00	1.00	3	-
GCF_002975205.1	s__Ochrobactrum sp002975205	88.4387	1354	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000182645.1	s__Ochrobactrum intermedium	87.9523	1233	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.99	97.16	0.92	0.84	56	-
GCF_006345815.1	s__Ochrobactrum sp006345815	87.7696	1224	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473915.1	s__Ochrobactrum sp900473915	87.56	1200	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470195.1	s__Ochrobactrum sp900470195	87.4818	1289	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.22	97.63	0.95	0.85	7	-
GCF_008932435.1	s__Ochrobactrum pseudintermedium	87.1804	1176	1732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	98.90	97.85	0.90	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:48,412] [INFO] GTDB search result was written to GCF_000017405.1_ASM1740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:48,412] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:48,416] [INFO] DFAST_QC result json was written to GCF_000017405.1_ASM1740v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:48,416] [INFO] DFAST_QC completed!
[2024-01-24 13:22:48,416] [INFO] Total running time: 0h1m37s