[2024-01-24 13:13:12,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,380] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4bed595-b3f8-4abe-8bfa-a0a6f3908a09/dqc_reference
[2024-01-24 13:13:13,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,838] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg258297be-7413-447b-893c-46cf28533998/GCF_002008165.1_ASM200816v1_genomic.fna.gz | prodigal -d GCF_002008165.1_ASM200816v1_genomic.fna/cds.fna -a GCF_002008165.1_ASM200816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:36,250] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:36,250] [INFO] Task started: HMMsearch
[2024-01-24 13:13:36,250] [INFO] Running command: hmmsearch --tblout GCF_002008165.1_ASM200816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4bed595-b3f8-4abe-8bfa-a0a6f3908a09/dqc_reference/reference_markers.hmm GCF_002008165.1_ASM200816v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:36,661] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:36,663] [INFO] Found 6/6 markers.
[2024-01-24 13:13:36,733] [INFO] Query marker FASTA was written to GCF_002008165.1_ASM200816v1_genomic.fna/markers.fasta
[2024-01-24 13:13:36,733] [INFO] Task started: Blastn
[2024-01-24 13:13:36,733] [INFO] Running command: blastn -query GCF_002008165.1_ASM200816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4bed595-b3f8-4abe-8bfa-a0a6f3908a09/dqc_reference/reference_markers.fasta -out GCF_002008165.1_ASM200816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:37,811] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:37,814] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:37,815] [INFO] Target genome list was writen to GCF_002008165.1_ASM200816v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:37,860] [INFO] Task started: fastANI
[2024-01-24 13:13:37,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg258297be-7413-447b-893c-46cf28533998/GCF_002008165.1_ASM200816v1_genomic.fna.gz --refList GCF_002008165.1_ASM200816v1_genomic.fna/target_genomes.txt --output GCF_002008165.1_ASM200816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:03,035] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4bed595-b3f8-4abe-8bfa-a0a6f3908a09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:03,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4bed595-b3f8-4abe-8bfa-a0a6f3908a09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:03,055] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:03,056] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:03,056] [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 laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	100.0	2421	2424	95	conclusive
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	99.9972	2417	2424	95	conclusive
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	93.9094	1977	2424	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	93.6533	1842	2424	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	93.4365	1936	2424	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	92.6999	1911	2424	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	92.223	1934	2424	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	92.173	1930	2424	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	92.1222	1863	2424	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	88.7189	1733	2424	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	88.0315	1652	2424	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.6322	1186	2424	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.3564	993	2424	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.2287	736	2424	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,058] [INFO] DFAST Taxonomy check result was written to GCF_002008165.1_ASM200816v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:03,058] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:03,058] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:03,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4bed595-b3f8-4abe-8bfa-a0a6f3908a09/dqc_reference/checkm_data
[2024-01-24 13:14:03,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:03,132] [INFO] Task started: CheckM
[2024-01-24 13:14:03,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002008165.1_ASM200816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002008165.1_ASM200816v1_genomic.fna/checkm_input GCF_002008165.1_ASM200816v1_genomic.fna/checkm_result
[2024-01-24 13:15:03,035] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:03,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:03,054] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:03,055] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:03,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002008165.1_ASM200816v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:03,055] [INFO] Task started: Blastn
[2024-01-24 13:15:03,056] [INFO] Running command: blastn -query GCF_002008165.1_ASM200816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4bed595-b3f8-4abe-8bfa-a0a6f3908a09/dqc_reference/reference_markers_gtdb.fasta -out GCF_002008165.1_ASM200816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:05,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:05,100] [INFO] Selected 12 target genomes.
[2024-01-24 13:15:05,100] [INFO] Target genome list was writen to GCF_002008165.1_ASM200816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:05,119] [INFO] Task started: fastANI
[2024-01-24 13:15:05,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg258297be-7413-447b-893c-46cf28533998/GCF_002008165.1_ASM200816v1_genomic.fna.gz --refList GCF_002008165.1_ASM200816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002008165.1_ASM200816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:27,493] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:27,506] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:27,506] [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_002008165.1	s__Rhizobium laguerreae	100.0	2421	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.33	95.04	0.87	0.82	51	conclusive
GCF_000009265.1	s__Rhizobium leguminosarum_L	94.2879	2022	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.59	95.46	0.90	0.82	60	-
GCF_004123835.1	s__Rhizobium leguminosarum_M	93.9307	1891	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005862305.2	s__Rhizobium indicum	93.9192	1976	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.44	95.15	0.91	0.82	6	-
GCF_013087515.1	s__Rhizobium sophorae	93.4365	1936	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.85	95.49	0.87	0.83	6	-
GCF_000023185.1	s__Rhizobium leguminosarum_J	93.2961	1936	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	97.68	0.92	0.88	6	-
GCF_000769405.2	s__Rhizobium leguminosarum_E	92.9801	1890	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.71	96.49	0.91	0.87	37	-
GCF_001652265.1	s__Rhizobium leguminosarum_D	92.7695	1890	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.67	97.67	0.88	0.88	3	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	92.7072	1910	2424	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	92.6264	1912	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.64	95.51	0.85	0.83	10	-
GCF_000371905.1	s__Rhizobium leguminosarum_I	92.4074	1846	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.88	97.75	0.91	0.88	6	-
GCF_002008365.1	s__Rhizobium leguminosarum	92.2089	1935	2424	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.98	97.38	0.91	0.86	85	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:27,508] [INFO] GTDB search result was written to GCF_002008165.1_ASM200816v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:27,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:27,511] [INFO] DFAST_QC result json was written to GCF_002008165.1_ASM200816v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:27,512] [INFO] DFAST_QC completed!
[2024-01-24 13:15:27,512] [INFO] Total running time: 0h2m15s