[2024-01-24 12:13:04,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:04,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:04,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg501ec14b-c46f-4329-8aa2-a48ce6b53d68/dqc_reference
[2024-01-24 12:13:05,958] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:05,959] [INFO] Task started: Prodigal
[2024-01-24 12:13:05,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ffd8bff-d680-4dcd-814c-8aaf536ae088/GCF_003010955.1_ASM301095v1_genomic.fna.gz | prodigal -d GCF_003010955.1_ASM301095v1_genomic.fna/cds.fna -a GCF_003010955.1_ASM301095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:23,309] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:23,309] [INFO] Task started: HMMsearch
[2024-01-24 12:13:23,310] [INFO] Running command: hmmsearch --tblout GCF_003010955.1_ASM301095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg501ec14b-c46f-4329-8aa2-a48ce6b53d68/dqc_reference/reference_markers.hmm GCF_003010955.1_ASM301095v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:23,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:23,553] [INFO] Found 6/6 markers.
[2024-01-24 12:13:23,597] [INFO] Query marker FASTA was written to GCF_003010955.1_ASM301095v1_genomic.fna/markers.fasta
[2024-01-24 12:13:23,598] [INFO] Task started: Blastn
[2024-01-24 12:13:23,598] [INFO] Running command: blastn -query GCF_003010955.1_ASM301095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg501ec14b-c46f-4329-8aa2-a48ce6b53d68/dqc_reference/reference_markers.fasta -out GCF_003010955.1_ASM301095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:24,361] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:24,366] [INFO] Selected 18 target genomes.
[2024-01-24 12:13:24,366] [INFO] Target genome list was writen to GCF_003010955.1_ASM301095v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:24,373] [INFO] Task started: fastANI
[2024-01-24 12:13:24,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ffd8bff-d680-4dcd-814c-8aaf536ae088/GCF_003010955.1_ASM301095v1_genomic.fna.gz --refList GCF_003010955.1_ASM301095v1_genomic.fna/target_genomes.txt --output GCF_003010955.1_ASM301095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:43,711] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:43,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg501ec14b-c46f-4329-8aa2-a48ce6b53d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:43,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg501ec14b-c46f-4329-8aa2-a48ce6b53d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:43,726] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:43,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:43,726] [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
Phyllobacterium brassicacearum	strain=STM 196	GCA_003010955.1	314235	314235	type	True	100.0	1888	1892	95	conclusive
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	83.2521	1295	1892	95	below_threshold
Phyllobacterium sophorae	strain=CCBAU 03422	GCA_003010965.1	1520277	1520277	type	True	82.2659	1159	1892	95	below_threshold
Phyllobacterium trifolii	strain=CECT 7015	GCA_014192095.1	300193	300193	type	True	81.5583	981	1892	95	below_threshold
Phyllobacterium bourgognense	strain=31-25a	GCA_003337575.1	314236	314236	type	True	81.298	991	1892	95	below_threshold
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	80.0904	823	1892	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	80.0852	823	1892	95	below_threshold
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	80.0742	797	1892	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	80.0141	826	1892	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.7471	361	1892	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	77.5806	361	1892	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.3346	338	1892	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	77.2582	350	1892	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	77.1311	336	1892	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.0402	331	1892	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.9392	252	1892	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.8181	236	1892	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.8089	237	1892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:43,729] [INFO] DFAST Taxonomy check result was written to GCF_003010955.1_ASM301095v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:43,729] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:43,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:43,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg501ec14b-c46f-4329-8aa2-a48ce6b53d68/dqc_reference/checkm_data
[2024-01-24 12:13:43,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:43,783] [INFO] Task started: CheckM
[2024-01-24 12:13:43,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003010955.1_ASM301095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003010955.1_ASM301095v1_genomic.fna/checkm_input GCF_003010955.1_ASM301095v1_genomic.fna/checkm_result
[2024-01-24 12:14:34,322] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:34,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:34,346] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:34,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:34,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003010955.1_ASM301095v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:34,347] [INFO] Task started: Blastn
[2024-01-24 12:14:34,347] [INFO] Running command: blastn -query GCF_003010955.1_ASM301095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg501ec14b-c46f-4329-8aa2-a48ce6b53d68/dqc_reference/reference_markers_gtdb.fasta -out GCF_003010955.1_ASM301095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:35,743] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:35,747] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:35,747] [INFO] Target genome list was writen to GCF_003010955.1_ASM301095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:35,757] [INFO] Task started: fastANI
[2024-01-24 12:14:35,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ffd8bff-d680-4dcd-814c-8aaf536ae088/GCF_003010955.1_ASM301095v1_genomic.fna.gz --refList GCF_003010955.1_ASM301095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003010955.1_ASM301095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:50,626] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:50,638] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:50,639] [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_003010955.1	s__Phyllobacterium brassicacearum	100.0	1888	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002764115.1	s__Phyllobacterium zundukense	83.2663	1293	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003010965.1	s__Phyllobacterium sophorae	82.2741	1156	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.00	98.48	0.92	0.90	3	-
GCF_014192095.1	s__Phyllobacterium trifolii	81.5465	983	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.32	99.28	0.88	0.88	4	-
GCF_003337575.1	s__Phyllobacterium bourgognense	81.3122	987	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473175.1	s__Phyllobacterium sp900473175	80.8165	915	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980555.1	s__Phyllobacterium myrsinacearum	80.0753	825	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.64	98.56	0.99	0.97	5	-
GCF_013327855.1	s__Phyllobacterium pellucidum	80.07	798	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	97.81	96.22	0.94	0.90	6	-
GCA_900539805.1	s__Phyllobacterium sp900539805	79.9668	800	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	96.69	96.69	0.93	0.93	2	-
GCF_014191375.1	s__Paramesorhizobium sp014191375	77.905	395	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900465915.1	s__63-22 sp900465915	77.5881	303	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22	95.0	97.55	97.55	0.92	0.92	2	-
GCF_003952465.1	s__Mesorhizobium sp003952465	77.3598	366	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_000350085.1	s__Mesorhizobium metallidurans	77.354	334	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:50,641] [INFO] GTDB search result was written to GCF_003010955.1_ASM301095v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:50,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:50,645] [INFO] DFAST_QC result json was written to GCF_003010955.1_ASM301095v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:50,645] [INFO] DFAST_QC completed!
[2024-01-24 12:14:50,645] [INFO] Total running time: 0h1m46s