[2024-01-25 18:43:05,732] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:05,734] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:05,734] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdfd7c4f-11d0-4ade-994a-e8922efd8e25/dqc_reference
[2024-01-25 18:43:06,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:06,889] [INFO] Task started: Prodigal
[2024-01-25 18:43:06,889] [INFO] Running command: gunzip -c /var/lib/cwl/stgea319be3-0419-4358-b139-cc8278be7981/GCF_002764115.1_ASM276411v1_genomic.fna.gz | prodigal -d GCF_002764115.1_ASM276411v1_genomic.fna/cds.fna -a GCF_002764115.1_ASM276411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:24,288] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:24,288] [INFO] Task started: HMMsearch
[2024-01-25 18:43:24,288] [INFO] Running command: hmmsearch --tblout GCF_002764115.1_ASM276411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdfd7c4f-11d0-4ade-994a-e8922efd8e25/dqc_reference/reference_markers.hmm GCF_002764115.1_ASM276411v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:24,559] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:24,560] [INFO] Found 6/6 markers.
[2024-01-25 18:43:24,611] [INFO] Query marker FASTA was written to GCF_002764115.1_ASM276411v1_genomic.fna/markers.fasta
[2024-01-25 18:43:24,611] [INFO] Task started: Blastn
[2024-01-25 18:43:24,611] [INFO] Running command: blastn -query GCF_002764115.1_ASM276411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdfd7c4f-11d0-4ade-994a-e8922efd8e25/dqc_reference/reference_markers.fasta -out GCF_002764115.1_ASM276411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:25,488] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:25,491] [INFO] Selected 15 target genomes.
[2024-01-25 18:43:25,491] [INFO] Target genome list was writen to GCF_002764115.1_ASM276411v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:25,513] [INFO] Task started: fastANI
[2024-01-25 18:43:25,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgea319be3-0419-4358-b139-cc8278be7981/GCF_002764115.1_ASM276411v1_genomic.fna.gz --refList GCF_002764115.1_ASM276411v1_genomic.fna/target_genomes.txt --output GCF_002764115.1_ASM276411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:43,541] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:43,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdfd7c4f-11d0-4ade-994a-e8922efd8e25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:43,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdfd7c4f-11d0-4ade-994a-e8922efd8e25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:43,553] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:43,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:43,553] [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 zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	100.0	2065	2066	95	conclusive
Phyllobacterium sophorae	strain=CCBAU 03422	GCA_003010965.1	1520277	1520277	type	True	86.1005	1350	2066	95	below_threshold
Phyllobacterium brassicacearum	strain=STM 196	GCA_003010955.1	314235	314235	type	True	83.2451	1297	2066	95	below_threshold
Phyllobacterium trifolii	strain=CECT 7015	GCA_014192095.1	300193	300193	type	True	81.8177	1046	2066	95	below_threshold
Phyllobacterium bourgognense	strain=31-25a	GCA_003337575.1	314236	314236	type	True	81.634	1047	2066	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	80.9326	891	2066	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	80.8067	893	2066	95	below_threshold
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	80.7497	886	2066	95	below_threshold
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	80.4855	860	2066	95	below_threshold
Phyllobacterium endophyticum	strain=PEPV15	GCA_003010935.1	1149773	1149773	type	True	80.1888	876	2066	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.8579	426	2066	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.5047	285	2066	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.4391	291	2066	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.4138	409	2066	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.2142	248	2066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:43,554] [INFO] DFAST Taxonomy check result was written to GCF_002764115.1_ASM276411v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:43,555] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:43,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:43,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdfd7c4f-11d0-4ade-994a-e8922efd8e25/dqc_reference/checkm_data
[2024-01-25 18:43:43,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:43,612] [INFO] Task started: CheckM
[2024-01-25 18:43:43,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002764115.1_ASM276411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002764115.1_ASM276411v1_genomic.fna/checkm_input GCF_002764115.1_ASM276411v1_genomic.fna/checkm_result
[2024-01-25 18:44:33,085] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:33,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:33,104] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:33,104] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:33,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002764115.1_ASM276411v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:33,105] [INFO] Task started: Blastn
[2024-01-25 18:44:33,105] [INFO] Running command: blastn -query GCF_002764115.1_ASM276411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdfd7c4f-11d0-4ade-994a-e8922efd8e25/dqc_reference/reference_markers_gtdb.fasta -out GCF_002764115.1_ASM276411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:34,873] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:34,876] [INFO] Selected 10 target genomes.
[2024-01-25 18:44:34,876] [INFO] Target genome list was writen to GCF_002764115.1_ASM276411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:34,899] [INFO] Task started: fastANI
[2024-01-25 18:44:34,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgea319be3-0419-4358-b139-cc8278be7981/GCF_002764115.1_ASM276411v1_genomic.fna.gz --refList GCF_002764115.1_ASM276411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002764115.1_ASM276411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:49,278] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:49,285] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:49,285] [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_002764115.1	s__Phyllobacterium zundukense	100.0	2064	2066	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_003010965.1	s__Phyllobacterium sophorae	86.0866	1351	2066	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_003010955.1	s__Phyllobacterium brassicacearum	83.2226	1301	2066	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_014192095.1	s__Phyllobacterium trifolii	81.814	1047	2066	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	-
GCA_900473175.1	s__Phyllobacterium sp900473175	81.7771	1038	2066	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_003337575.1	s__Phyllobacterium bourgognense	81.6211	1050	2066	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_017833775.1	s__Phyllobacterium sp017833775	81.0246	980	2066	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	80.7878	896	2066	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	-
GCA_900539805.1	s__Phyllobacterium sp900539805	80.7189	864	2066	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_013327855.1	s__Phyllobacterium pellucidum	80.4817	861	2066	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:49,287] [INFO] GTDB search result was written to GCF_002764115.1_ASM276411v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:49,288] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:49,290] [INFO] DFAST_QC result json was written to GCF_002764115.1_ASM276411v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:49,291] [INFO] DFAST_QC completed!
[2024-01-25 18:44:49,291] [INFO] Total running time: 0h1m44s