[2024-01-25 17:44:05,771] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:05,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:05,774] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb658825-56b7-4e7f-97c0-42ddd9ff35a1/dqc_reference
[2024-01-25 17:44:06,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:06,919] [INFO] Task started: Prodigal
[2024-01-25 17:44:06,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg19dd7bdd-fdba-4a20-98eb-da6949e73852/GCF_014640615.1_ASM1464061v1_genomic.fna.gz | prodigal -d GCF_014640615.1_ASM1464061v1_genomic.fna/cds.fna -a GCF_014640615.1_ASM1464061v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:19,915] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:19,915] [INFO] Task started: HMMsearch
[2024-01-25 17:44:19,915] [INFO] Running command: hmmsearch --tblout GCF_014640615.1_ASM1464061v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb658825-56b7-4e7f-97c0-42ddd9ff35a1/dqc_reference/reference_markers.hmm GCF_014640615.1_ASM1464061v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:20,234] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:20,237] [INFO] Found 6/6 markers.
[2024-01-25 17:44:20,279] [INFO] Query marker FASTA was written to GCF_014640615.1_ASM1464061v1_genomic.fna/markers.fasta
[2024-01-25 17:44:20,280] [INFO] Task started: Blastn
[2024-01-25 17:44:20,280] [INFO] Running command: blastn -query GCF_014640615.1_ASM1464061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb658825-56b7-4e7f-97c0-42ddd9ff35a1/dqc_reference/reference_markers.fasta -out GCF_014640615.1_ASM1464061v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:21,209] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:21,212] [INFO] Selected 18 target genomes.
[2024-01-25 17:44:21,212] [INFO] Target genome list was writen to GCF_014640615.1_ASM1464061v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:21,221] [INFO] Task started: fastANI
[2024-01-25 17:44:21,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg19dd7bdd-fdba-4a20-98eb-da6949e73852/GCF_014640615.1_ASM1464061v1_genomic.fna.gz --refList GCF_014640615.1_ASM1464061v1_genomic.fna/target_genomes.txt --output GCF_014640615.1_ASM1464061v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:40,701] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:40,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb658825-56b7-4e7f-97c0-42ddd9ff35a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:40,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb658825-56b7-4e7f-97c0-42ddd9ff35a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:40,712] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:44:40,713] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:44:40,713] [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 leguminum	strain=ORS 1419	GCA_003217235.1	314237	314237	type	True	83.5719	908	1606	95	below_threshold
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	81.7882	851	1606	95	below_threshold
Phyllobacterium salinisoli	strain=LLAN61	GCA_003335045.1	1899321	1899321	type	True	81.5955	827	1606	95	below_threshold
Brucella daejeonensis	strain=DSM 26944	GCA_014199265.1	659015	659015	type	True	79.0254	505	1606	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	78.6736	502	1606	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	78.5333	448	1606	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	78.5109	416	1606	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.4945	465	1606	95	below_threshold
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	78.4903	461	1606	95	below_threshold
Brucella haematophila	strain=CCUG 38531	GCA_005938105.1	419474	419474	type	True	78.4223	452	1606	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	78.3951	428	1606	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	78.3641	473	1606	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.284	456	1606	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	78.2715	448	1606	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.0453	366	1606	95	below_threshold
Phyllobacterium brassicacearum	strain=STM 196	GCA_003010955.1	314235	314235	type	True	77.5984	329	1606	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.5801	358	1606	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.5773	359	1606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:40,714] [INFO] DFAST Taxonomy check result was written to GCF_014640615.1_ASM1464061v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:40,715] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:40,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:40,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb658825-56b7-4e7f-97c0-42ddd9ff35a1/dqc_reference/checkm_data
[2024-01-25 17:44:40,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:40,764] [INFO] Task started: CheckM
[2024-01-25 17:44:40,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640615.1_ASM1464061v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640615.1_ASM1464061v1_genomic.fna/checkm_input GCF_014640615.1_ASM1464061v1_genomic.fna/checkm_result
[2024-01-25 17:45:18,622] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:18,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:18,637] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:18,637] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:18,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640615.1_ASM1464061v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:18,638] [INFO] Task started: Blastn
[2024-01-25 17:45:18,638] [INFO] Running command: blastn -query GCF_014640615.1_ASM1464061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb658825-56b7-4e7f-97c0-42ddd9ff35a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640615.1_ASM1464061v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:20,454] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:20,457] [INFO] Selected 8 target genomes.
[2024-01-25 17:45:20,457] [INFO] Target genome list was writen to GCF_014640615.1_ASM1464061v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:20,468] [INFO] Task started: fastANI
[2024-01-25 17:45:20,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg19dd7bdd-fdba-4a20-98eb-da6949e73852/GCF_014640615.1_ASM1464061v1_genomic.fna.gz --refList GCF_014640615.1_ASM1464061v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640615.1_ASM1464061v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:31,943] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:31,949] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:31,949] [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_014640615.1	s__Paramesorhizobium endophyticum	100.0	1603	1606	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	conclusive
GCF_014191375.1	s__Paramesorhizobium sp014191375	83.7105	931	1606	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	-
GCF_003217235.1	s__Paramesorhizobium leguminum	83.5829	907	1606	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	-
GCF_001558695.1	s__Paramesorhizobium deserti	82.4626	898	1606	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	-
GCF_002980495.1	s__Paramesorhizobium phragmitis	81.7844	852	1606	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	-
GCF_003335045.1	s__Paramesorhizobium salinisoli	81.579	830	1606	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_001898995.1	s__63-22 sp001898995	79.8909	560	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014192095.1	s__Phyllobacterium trifolii	77.4087	297	1606	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:31,950] [INFO] GTDB search result was written to GCF_014640615.1_ASM1464061v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:31,951] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:31,954] [INFO] DFAST_QC result json was written to GCF_014640615.1_ASM1464061v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:31,954] [INFO] DFAST_QC completed!
[2024-01-25 17:45:31,954] [INFO] Total running time: 0h1m26s