[2024-01-24 14:30:17,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:17,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:17,359] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c7256f9-cc10-4d25-bfb1-ae574e12abc2/dqc_reference
[2024-01-24 14:30:18,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,695] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,695] [INFO] Running command: gunzip -c /var/lib/cwl/stgb83545d3-91b9-4716-83fd-c90aa268616e/GCF_003985145.1_ASM398514v1_genomic.fna.gz | prodigal -d GCF_003985145.1_ASM398514v1_genomic.fna/cds.fna -a GCF_003985145.1_ASM398514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:40,387] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:40,387] [INFO] Task started: HMMsearch
[2024-01-24 14:30:40,388] [INFO] Running command: hmmsearch --tblout GCF_003985145.1_ASM398514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c7256f9-cc10-4d25-bfb1-ae574e12abc2/dqc_reference/reference_markers.hmm GCF_003985145.1_ASM398514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:40,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:40,749] [INFO] Found 6/6 markers.
[2024-01-24 14:30:40,811] [INFO] Query marker FASTA was written to GCF_003985145.1_ASM398514v1_genomic.fna/markers.fasta
[2024-01-24 14:30:40,812] [INFO] Task started: Blastn
[2024-01-24 14:30:40,812] [INFO] Running command: blastn -query GCF_003985145.1_ASM398514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c7256f9-cc10-4d25-bfb1-ae574e12abc2/dqc_reference/reference_markers.fasta -out GCF_003985145.1_ASM398514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:41,910] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:41,914] [INFO] Selected 21 target genomes.
[2024-01-24 14:30:41,915] [INFO] Target genome list was writen to GCF_003985145.1_ASM398514v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:41,934] [INFO] Task started: fastANI
[2024-01-24 14:30:41,935] [INFO] Running command: fastANI --query /var/lib/cwl/stgb83545d3-91b9-4716-83fd-c90aa268616e/GCF_003985145.1_ASM398514v1_genomic.fna.gz --refList GCF_003985145.1_ASM398514v1_genomic.fna/target_genomes.txt --output GCF_003985145.1_ASM398514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:19,557] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:19,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c7256f9-cc10-4d25-bfb1-ae574e12abc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:19,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c7256f9-cc10-4d25-bfb1-ae574e12abc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:19,578] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:19,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:19,578] [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 anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	100.0	2354	2356	95	conclusive
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	99.9959	2346	2356	95	conclusive
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	91.532	1924	2356	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	91.2896	1903	2356	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	91.2345	1738	2356	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	91.1821	1896	2356	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	90.9281	1846	2356	95	below_threshold
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	90.7196	1804	2356	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	90.7037	1809	2356	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	89.0768	1771	2356	95	below_threshold
Rhizobium fabae	strain=DSM 19331	GCA_014196235.1	573179	573179	type	True	89.0532	1761	2356	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002914525.1	1538159	1538159	type	True	88.9609	1720	2356	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002531855.1	1538159	1538159	type	True	88.9558	1721	2356	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	88.8767	1708	2356	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	88.6676	1667	2356	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	88.3486	1630	2356	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	87.9413	1630	2356	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	87.4232	1623	2356	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.8084	1221	2356	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.566	1015	2356	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.1825	761	2356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:19,580] [INFO] DFAST Taxonomy check result was written to GCF_003985145.1_ASM398514v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:19,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:19,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:19,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c7256f9-cc10-4d25-bfb1-ae574e12abc2/dqc_reference/checkm_data
[2024-01-24 14:31:19,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:19,652] [INFO] Task started: CheckM
[2024-01-24 14:31:19,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003985145.1_ASM398514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003985145.1_ASM398514v1_genomic.fna/checkm_input GCF_003985145.1_ASM398514v1_genomic.fna/checkm_result
[2024-01-24 14:32:20,700] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:20,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:20,727] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:20,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:20,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003985145.1_ASM398514v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:20,729] [INFO] Task started: Blastn
[2024-01-24 14:32:20,729] [INFO] Running command: blastn -query GCF_003985145.1_ASM398514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c7256f9-cc10-4d25-bfb1-ae574e12abc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003985145.1_ASM398514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:22,841] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:22,845] [INFO] Selected 20 target genomes.
[2024-01-24 14:32:22,846] [INFO] Target genome list was writen to GCF_003985145.1_ASM398514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:22,860] [INFO] Task started: fastANI
[2024-01-24 14:32:22,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgb83545d3-91b9-4716-83fd-c90aa268616e/GCF_003985145.1_ASM398514v1_genomic.fna.gz --refList GCF_003985145.1_ASM398514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003985145.1_ASM398514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:58,367] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:58,385] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:58,386] [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_003985145.1	s__Rhizobium anhuiense	100.0	2354	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	conclusive
GCF_004123835.1	s__Rhizobium leguminosarum_M	91.3265	1805	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	91.2957	1903	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.01	96.15	0.89	0.84	170	-
GCF_005862305.2	s__Rhizobium indicum	91.1983	1894	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.44	95.15	0.91	0.82	6	-
GCF_014198335.1	s__Rhizobium leguminosarum_N	91.0761	1627	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.95	99.93	0.95	0.91	10	-
GCF_000769405.2	s__Rhizobium leguminosarum_E	91.0597	1863	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.71	96.49	0.91	0.87	37	-
GCF_000009265.1	s__Rhizobium leguminosarum_L	91.0338	1912	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.59	95.46	0.90	0.82	60	-
GCF_001657485.1	s__Rhizobium sp001657485	91.0336	1862	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.95	97.95	0.90	0.90	2	-
GCF_001652265.1	s__Rhizobium leguminosarum_D	91.0135	1812	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.67	97.67	0.88	0.88	3	-
GCF_002531725.1	s__Rhizobium sp002531725	90.9813	1824	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013087515.1	s__Rhizobium sophorae	90.9413	1844	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.85	95.49	0.87	0.83	6	-
GCF_002008165.1	s__Rhizobium laguerreae	90.7036	1809	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.33	95.04	0.87	0.82	51	-
GCF_000371905.1	s__Rhizobium leguminosarum_I	90.6297	1751	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.88	97.75	0.91	0.88	6	-
GCF_017876795.1	s__Rhizobium leguminosarum_P	89.3363	1741	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172795.2	s__Rhizobium sp000172795	89.186	1622	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271845.1	s__Rhizobium leguminosarum_G	89.0485	1771	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002914525.1	s__Rhizobium hidalgonense	88.9641	1720	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.87	98.55	0.90	0.84	6	-
GCF_014193025.1	s__Rhizobium sp014193025	88.8051	1591	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003985155.1	s__Rhizobium vallis	88.6417	1671	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094625.1	s__Rhizobium aethiopicum	87.4185	1623	2356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.33	98.33	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:58,387] [INFO] GTDB search result was written to GCF_003985145.1_ASM398514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:58,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:58,396] [INFO] DFAST_QC result json was written to GCF_003985145.1_ASM398514v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:58,396] [INFO] DFAST_QC completed!
[2024-01-24 14:32:58,396] [INFO] Total running time: 0h2m41s