[2024-01-24 11:26:27,645] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:27,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:27,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg22811d06-0482-4a21-86ba-72a897bf0d9d/dqc_reference
[2024-01-24 11:26:29,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,267] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,268] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3c1c9a2-b99d-4a28-842b-0e7f518eae21/GCF_003217235.1_ASM321723v1_genomic.fna.gz | prodigal -d GCF_003217235.1_ASM321723v1_genomic.fna/cds.fna -a GCF_003217235.1_ASM321723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:40,323] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:40,324] [INFO] Task started: HMMsearch
[2024-01-24 11:26:40,324] [INFO] Running command: hmmsearch --tblout GCF_003217235.1_ASM321723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22811d06-0482-4a21-86ba-72a897bf0d9d/dqc_reference/reference_markers.hmm GCF_003217235.1_ASM321723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:40,638] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:40,639] [INFO] Found 6/6 markers.
[2024-01-24 11:26:40,674] [INFO] Query marker FASTA was written to GCF_003217235.1_ASM321723v1_genomic.fna/markers.fasta
[2024-01-24 11:26:40,674] [INFO] Task started: Blastn
[2024-01-24 11:26:40,675] [INFO] Running command: blastn -query GCF_003217235.1_ASM321723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22811d06-0482-4a21-86ba-72a897bf0d9d/dqc_reference/reference_markers.fasta -out GCF_003217235.1_ASM321723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:41,598] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:41,601] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:41,601] [INFO] Target genome list was writen to GCF_003217235.1_ASM321723v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:41,607] [INFO] Task started: fastANI
[2024-01-24 11:26:41,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3c1c9a2-b99d-4a28-842b-0e7f518eae21/GCF_003217235.1_ASM321723v1_genomic.fna.gz --refList GCF_003217235.1_ASM321723v1_genomic.fna/target_genomes.txt --output GCF_003217235.1_ASM321723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:00,195] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:00,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22811d06-0482-4a21-86ba-72a897bf0d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:00,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22811d06-0482-4a21-86ba-72a897bf0d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:00,211] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:00,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:00,211] [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	100.0	1207	1212	95	conclusive
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	82.9806	794	1212	95	below_threshold
Phyllobacterium salinisoli	strain=LLAN61	GCA_003335045.1	1899321	1899321	type	True	82.8359	790	1212	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	78.8862	419	1212	95	below_threshold
Brucella daejeonensis	strain=DSM 26944	GCA_014199265.1	659015	659015	type	True	78.7785	446	1212	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	78.4401	419	1212	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	78.3906	442	1212	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	78.3822	447	1212	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	78.2811	413	1212	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.2539	422	1212	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.2007	393	1212	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	78.173	413	1212	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	78.0349	301	1212	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.9612	310	1212	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.8137	301	1212	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.8128	301	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:00,213] [INFO] DFAST Taxonomy check result was written to GCF_003217235.1_ASM321723v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:00,214] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:00,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:00,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22811d06-0482-4a21-86ba-72a897bf0d9d/dqc_reference/checkm_data
[2024-01-24 11:27:00,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:00,264] [INFO] Task started: CheckM
[2024-01-24 11:27:00,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217235.1_ASM321723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217235.1_ASM321723v1_genomic.fna/checkm_input GCF_003217235.1_ASM321723v1_genomic.fna/checkm_result
[2024-01-24 11:27:36,992] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:36,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,016] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:37,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:37,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217235.1_ASM321723v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:37,018] [INFO] Task started: Blastn
[2024-01-24 11:27:37,018] [INFO] Running command: blastn -query GCF_003217235.1_ASM321723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22811d06-0482-4a21-86ba-72a897bf0d9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217235.1_ASM321723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:38,705] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:38,718] [INFO] Selected 6 target genomes.
[2024-01-24 11:27:38,718] [INFO] Target genome list was writen to GCF_003217235.1_ASM321723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:38,725] [INFO] Task started: fastANI
[2024-01-24 11:27:38,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3c1c9a2-b99d-4a28-842b-0e7f518eae21/GCF_003217235.1_ASM321723v1_genomic.fna.gz --refList GCF_003217235.1_ASM321723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217235.1_ASM321723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:47,336] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:47,349] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:47,349] [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_003217235.1	s__Paramesorhizobium leguminum	100.0	1207	1212	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_014640615.1	s__Paramesorhizobium endophyticum	83.7107	890	1212	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_014191375.1	s__Paramesorhizobium sp014191375	83.2467	825	1212	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	82.9298	800	1212	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	82.8594	789	1212	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	82.818	820	1212	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:47,351] [INFO] GTDB search result was written to GCF_003217235.1_ASM321723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:47,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:47,355] [INFO] DFAST_QC result json was written to GCF_003217235.1_ASM321723v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:47,355] [INFO] DFAST_QC completed!
[2024-01-24 11:27:47,355] [INFO] Total running time: 0h1m20s