[2024-01-25 19:04:05,570] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:05,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:05,572] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa0a645f-75c4-4dec-855d-4c8231ac0d63/dqc_reference
[2024-01-25 19:04:06,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:06,673] [INFO] Task started: Prodigal
[2024-01-25 19:04:06,673] [INFO] Running command: gunzip -c /var/lib/cwl/stgf80ecc6a-e415-4f73-b615-3052d3e5ed0e/GCF_025941625.1_ASM2594162v1_genomic.fna.gz | prodigal -d GCF_025941625.1_ASM2594162v1_genomic.fna/cds.fna -a GCF_025941625.1_ASM2594162v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:27,402] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:27,402] [INFO] Task started: HMMsearch
[2024-01-25 19:04:27,402] [INFO] Running command: hmmsearch --tblout GCF_025941625.1_ASM2594162v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa0a645f-75c4-4dec-855d-4c8231ac0d63/dqc_reference/reference_markers.hmm GCF_025941625.1_ASM2594162v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:27,711] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:27,712] [INFO] Found 6/6 markers.
[2024-01-25 19:04:27,775] [INFO] Query marker FASTA was written to GCF_025941625.1_ASM2594162v1_genomic.fna/markers.fasta
[2024-01-25 19:04:27,775] [INFO] Task started: Blastn
[2024-01-25 19:04:27,775] [INFO] Running command: blastn -query GCF_025941625.1_ASM2594162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa0a645f-75c4-4dec-855d-4c8231ac0d63/dqc_reference/reference_markers.fasta -out GCF_025941625.1_ASM2594162v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:28,737] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:28,740] [INFO] Selected 15 target genomes.
[2024-01-25 19:04:28,740] [INFO] Target genome list was writen to GCF_025941625.1_ASM2594162v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:28,754] [INFO] Task started: fastANI
[2024-01-25 19:04:28,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgf80ecc6a-e415-4f73-b615-3052d3e5ed0e/GCF_025941625.1_ASM2594162v1_genomic.fna.gz --refList GCF_025941625.1_ASM2594162v1_genomic.fna/target_genomes.txt --output GCF_025941625.1_ASM2594162v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:55,787] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:55,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa0a645f-75c4-4dec-855d-4c8231ac0d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:55,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa0a645f-75c4-4dec-855d-4c8231ac0d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:55,797] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:04:55,797] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:04:55,798] [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
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	94.6054	2019	2627	95	below_threshold
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	94.0986	1967	2627	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	94.0975	1966	2627	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	93.7	1848	2627	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	93.5982	1988	2627	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	93.5152	1951	2627	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	92.7165	1969	2627	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	92.7039	1979	2627	95	below_threshold
Rhizobium leguminosarum	strain=DSM 106839	GCA_014202125.1	384	384	suspected-type	True	92.6557	1980	2627	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	92.6486	1920	2627	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	88.9214	1766	2627	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	88.0504	1631	2627	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.6632	1183	2627	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.4493	1006	2627	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.4644	685	2627	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:55,799] [INFO] DFAST Taxonomy check result was written to GCF_025941625.1_ASM2594162v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:55,800] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:55,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:55,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa0a645f-75c4-4dec-855d-4c8231ac0d63/dqc_reference/checkm_data
[2024-01-25 19:04:55,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:55,873] [INFO] Task started: CheckM
[2024-01-25 19:04:55,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025941625.1_ASM2594162v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025941625.1_ASM2594162v1_genomic.fna/checkm_input GCF_025941625.1_ASM2594162v1_genomic.fna/checkm_result
[2024-01-25 19:05:52,800] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:52,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:52,820] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:52,820] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:52,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025941625.1_ASM2594162v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:52,821] [INFO] Task started: Blastn
[2024-01-25 19:05:52,821] [INFO] Running command: blastn -query GCF_025941625.1_ASM2594162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa0a645f-75c4-4dec-855d-4c8231ac0d63/dqc_reference/reference_markers_gtdb.fasta -out GCF_025941625.1_ASM2594162v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:54,841] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:54,843] [INFO] Selected 12 target genomes.
[2024-01-25 19:05:54,843] [INFO] Target genome list was writen to GCF_025941625.1_ASM2594162v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:54,858] [INFO] Task started: fastANI
[2024-01-25 19:05:54,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgf80ecc6a-e415-4f73-b615-3052d3e5ed0e/GCF_025941625.1_ASM2594162v1_genomic.fna.gz --refList GCF_025941625.1_ASM2594162v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025941625.1_ASM2594162v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:19,163] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:19,171] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:19,172] [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_000009265.1	s__Rhizobium leguminosarum_L	95.9014	2122	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.59	95.46	0.90	0.82	60	conclusive
GCF_005862305.2	s__Rhizobium indicum	94.6054	2019	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.44	95.15	0.91	0.82	6	-
GCF_004123835.1	s__Rhizobium leguminosarum_M	94.1039	1946	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008165.1	s__Rhizobium laguerreae	94.0975	1966	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.33	95.04	0.87	0.82	51	-
GCF_000023185.1	s__Rhizobium leguminosarum_J	94.0413	2005	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	97.68	0.92	0.88	6	-
GCF_001657485.1	s__Rhizobium sp001657485	94.0319	2034	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.95	97.95	0.90	0.90	2	-
GCF_000769405.2	s__Rhizobium leguminosarum_E	93.727	1935	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.71	96.49	0.91	0.87	37	-
GCF_013087515.1	s__Rhizobium sophorae	93.6118	1986	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.85	95.49	0.87	0.83	6	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	93.5152	1951	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.01	96.15	0.89	0.84	170	-
GCF_002953715.1	s__Rhizobium leguminosarum_K	93.1375	1964	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.64	95.51	0.85	0.83	10	-
GCF_001652265.1	s__Rhizobium leguminosarum_D	92.9251	1893	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.67	97.67	0.88	0.88	3	-
GCF_002008365.1	s__Rhizobium leguminosarum	92.7085	1970	2627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.98	97.38	0.91	0.86	85	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:19,174] [INFO] GTDB search result was written to GCF_025941625.1_ASM2594162v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:19,174] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:19,178] [INFO] DFAST_QC result json was written to GCF_025941625.1_ASM2594162v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:19,178] [INFO] DFAST_QC completed!
[2024-01-25 19:06:19,178] [INFO] Total running time: 0h2m14s