[2024-01-24 11:26:07,916] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:07,918] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:07,918] [INFO] DQC Reference Directory: /var/lib/cwl/stgda2022f8-d7f2-4fc3-a47e-9c5101150143/dqc_reference
[2024-01-24 11:26:09,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:09,152] [INFO] Task started: Prodigal
[2024-01-24 11:26:09,153] [INFO] Running command: gunzip -c /var/lib/cwl/stge92a55f4-b23f-460d-bc41-4dfd424de804/GCF_003337575.1_ASM333757v1_genomic.fna.gz | prodigal -d GCF_003337575.1_ASM333757v1_genomic.fna/cds.fna -a GCF_003337575.1_ASM333757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:26,442] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:26,442] [INFO] Task started: HMMsearch
[2024-01-24 11:26:26,442] [INFO] Running command: hmmsearch --tblout GCF_003337575.1_ASM333757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda2022f8-d7f2-4fc3-a47e-9c5101150143/dqc_reference/reference_markers.hmm GCF_003337575.1_ASM333757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:26,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:26,811] [INFO] Found 6/6 markers.
[2024-01-24 11:26:26,869] [INFO] Query marker FASTA was written to GCF_003337575.1_ASM333757v1_genomic.fna/markers.fasta
[2024-01-24 11:26:26,870] [INFO] Task started: Blastn
[2024-01-24 11:26:26,870] [INFO] Running command: blastn -query GCF_003337575.1_ASM333757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda2022f8-d7f2-4fc3-a47e-9c5101150143/dqc_reference/reference_markers.fasta -out GCF_003337575.1_ASM333757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:27,771] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:27,775] [INFO] Selected 15 target genomes.
[2024-01-24 11:26:27,775] [INFO] Target genome list was writen to GCF_003337575.1_ASM333757v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:27,781] [INFO] Task started: fastANI
[2024-01-24 11:26:27,781] [INFO] Running command: fastANI --query /var/lib/cwl/stge92a55f4-b23f-460d-bc41-4dfd424de804/GCF_003337575.1_ASM333757v1_genomic.fna.gz --refList GCF_003337575.1_ASM333757v1_genomic.fna/target_genomes.txt --output GCF_003337575.1_ASM333757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:45,230] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:45,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda2022f8-d7f2-4fc3-a47e-9c5101150143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:45,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda2022f8-d7f2-4fc3-a47e-9c5101150143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:45,244] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:45,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:45,244] [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 bourgognense	strain=31-25a	GCA_003337575.1	314236	314236	type	True	100.0	1844	1849	95	conclusive
Phyllobacterium trifolii	strain=CECT 7015	GCA_014192095.1	300193	300193	type	True	92.4168	1509	1849	95	below_threshold
Phyllobacterium endophyticum	strain=PEPV15	GCA_003010935.1	1149773	1149773	type	True	82.7228	1184	1849	95	below_threshold
Phyllobacterium endophyticum	strain=CECT 7949	GCA_014192255.1	1149773	1149773	type	True	82.6662	1180	1849	95	below_threshold
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	81.656	1031	1849	95	below_threshold
Phyllobacterium brassicacearum	strain=STM 196	GCA_003010955.1	314235	314235	type	True	81.6041	945	1849	95	below_threshold
Phyllobacterium sophorae	strain=CCBAU 03422	GCA_003010965.1	1520277	1520277	type	True	80.9105	1002	1849	95	below_threshold
Phyllobacterium leguminum	strain=ORS 1419	GCA_003217235.1	314237	314237	type	True	77.6659	283	1849	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.3921	330	1849	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.2975	289	1849	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.059	206	1849	95	below_threshold
Rhizobium halophytocola	strain=DSM 21600	GCA_017873095.1	735519	735519	type	True	76.9521	215	1849	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.9048	197	1849	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	76.772	185	1849	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:45,246] [INFO] DFAST Taxonomy check result was written to GCF_003337575.1_ASM333757v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:45,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:45,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:45,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda2022f8-d7f2-4fc3-a47e-9c5101150143/dqc_reference/checkm_data
[2024-01-24 11:26:45,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:45,309] [INFO] Task started: CheckM
[2024-01-24 11:26:45,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337575.1_ASM333757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337575.1_ASM333757v1_genomic.fna/checkm_input GCF_003337575.1_ASM333757v1_genomic.fna/checkm_result
[2024-01-24 11:27:37,241] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:37,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,267] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:37,267] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:37,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337575.1_ASM333757v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:37,268] [INFO] Task started: Blastn
[2024-01-24 11:27:37,268] [INFO] Running command: blastn -query GCF_003337575.1_ASM333757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda2022f8-d7f2-4fc3-a47e-9c5101150143/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337575.1_ASM333757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:38,927] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:38,932] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:38,932] [INFO] Target genome list was writen to GCF_003337575.1_ASM333757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:38,939] [INFO] Task started: fastANI
[2024-01-24 11:27:38,940] [INFO] Running command: fastANI --query /var/lib/cwl/stge92a55f4-b23f-460d-bc41-4dfd424de804/GCF_003337575.1_ASM333757v1_genomic.fna.gz --refList GCF_003337575.1_ASM333757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337575.1_ASM333757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:50,175] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:50,189] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:50,189] [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_003337575.1	s__Phyllobacterium bourgognense	100.0	1844	1849	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	conclusive
GCF_014192095.1	s__Phyllobacterium trifolii	92.4361	1507	1849	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_017833775.1	s__Phyllobacterium sp017833775	90.2873	1402	1849	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_003010935.1	s__Phyllobacterium endophyticum	82.7274	1183	1849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.50	98.51	0.95	0.87	4	-
GCF_002764115.1	s__Phyllobacterium zundukense	81.6567	1031	1849	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_003010955.1	s__Phyllobacterium brassicacearum	81.6159	943	1849	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	80.9132	1002	1849	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_003217235.1	s__Paramesorhizobium leguminum	77.6543	284	1849	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_002706335.1	s__Oricola sp002706335	76.6357	170	1849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:50,191] [INFO] GTDB search result was written to GCF_003337575.1_ASM333757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:50,191] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:50,195] [INFO] DFAST_QC result json was written to GCF_003337575.1_ASM333757v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:50,195] [INFO] DFAST_QC completed!
[2024-01-24 11:27:50,195] [INFO] Total running time: 0h1m42s