[2024-01-25 18:25:20,520] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:20,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:20,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b51777b-6986-4742-a642-a6639e60e876/dqc_reference
[2024-01-25 18:25:21,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:21,659] [INFO] Task started: Prodigal
[2024-01-25 18:25:21,659] [INFO] Running command: gunzip -c /var/lib/cwl/stgd72d9588-b2e2-4675-a144-23eba445e8f5/GCF_002531935.1_ASM253193v1_genomic.fna.gz | prodigal -d GCF_002531935.1_ASM253193v1_genomic.fna/cds.fna -a GCF_002531935.1_ASM253193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:39,107] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:39,107] [INFO] Task started: HMMsearch
[2024-01-25 18:25:39,107] [INFO] Running command: hmmsearch --tblout GCF_002531935.1_ASM253193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b51777b-6986-4742-a642-a6639e60e876/dqc_reference/reference_markers.hmm GCF_002531935.1_ASM253193v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:39,394] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:39,395] [INFO] Found 6/6 markers.
[2024-01-25 18:25:39,448] [INFO] Query marker FASTA was written to GCF_002531935.1_ASM253193v1_genomic.fna/markers.fasta
[2024-01-25 18:25:39,448] [INFO] Task started: Blastn
[2024-01-25 18:25:39,448] [INFO] Running command: blastn -query GCF_002531935.1_ASM253193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b51777b-6986-4742-a642-a6639e60e876/dqc_reference/reference_markers.fasta -out GCF_002531935.1_ASM253193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:40,429] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:40,432] [INFO] Selected 20 target genomes.
[2024-01-25 18:25:40,432] [INFO] Target genome list was writen to GCF_002531935.1_ASM253193v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:40,444] [INFO] Task started: fastANI
[2024-01-25 18:25:40,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgd72d9588-b2e2-4675-a144-23eba445e8f5/GCF_002531935.1_ASM253193v1_genomic.fna.gz --refList GCF_002531935.1_ASM253193v1_genomic.fna/target_genomes.txt --output GCF_002531935.1_ASM253193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:26:13,772] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:13,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b51777b-6986-4742-a642-a6639e60e876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:26:13,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b51777b-6986-4742-a642-a6639e60e876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:26:13,786] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:26:13,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:26:13,786] [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 chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	100.0	2245	2252	95	conclusive
Rhizobium hidalgonense	strain=FH14	GCA_002914525.1	1538159	1538159	type	True	90.9559	1770	2252	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002531855.1	1538159	1538159	type	True	90.9465	1771	2252	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	90.5033	1706	2252	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	89.9531	1767	2252	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	89.5825	1717	2252	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	89.5523	1720	2252	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	89.4574	1743	2252	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	89.2742	1571	2252	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	89.0646	1694	2252	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	89.0504	1686	2252	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	88.9687	1658	2252	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	88.9429	1661	2252	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	88.8476	1617	2252	95	below_threshold
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	88.7842	1639	2252	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	88.7663	1694	2252	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	88.5541	1654	2252	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.4157	1163	2252	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.615	1008	2252	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.5804	688	2252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:26:13,788] [INFO] DFAST Taxonomy check result was written to GCF_002531935.1_ASM253193v1_genomic.fna/tc_result.tsv
[2024-01-25 18:26:13,788] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:26:13,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:26:13,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b51777b-6986-4742-a642-a6639e60e876/dqc_reference/checkm_data
[2024-01-25 18:26:13,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:26:13,857] [INFO] Task started: CheckM
[2024-01-25 18:26:13,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002531935.1_ASM253193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002531935.1_ASM253193v1_genomic.fna/checkm_input GCF_002531935.1_ASM253193v1_genomic.fna/checkm_result
[2024-01-25 18:27:02,890] [INFO] Task succeeded: CheckM
[2024-01-25 18:27:02,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:27:02,909] [INFO] ===== Completeness check finished =====
[2024-01-25 18:27:02,910] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:27:02,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002531935.1_ASM253193v1_genomic.fna/markers.fasta)
[2024-01-25 18:27:02,910] [INFO] Task started: Blastn
[2024-01-25 18:27:02,910] [INFO] Running command: blastn -query GCF_002531935.1_ASM253193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b51777b-6986-4742-a642-a6639e60e876/dqc_reference/reference_markers_gtdb.fasta -out GCF_002531935.1_ASM253193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:27:05,007] [INFO] Task succeeded: Blastn
[2024-01-25 18:27:05,011] [INFO] Selected 18 target genomes.
[2024-01-25 18:27:05,012] [INFO] Target genome list was writen to GCF_002531935.1_ASM253193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:27:05,036] [INFO] Task started: fastANI
[2024-01-25 18:27:05,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgd72d9588-b2e2-4675-a144-23eba445e8f5/GCF_002531935.1_ASM253193v1_genomic.fna.gz --refList GCF_002531935.1_ASM253193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002531935.1_ASM253193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:27:36,815] [INFO] Task succeeded: fastANI
[2024-01-25 18:27:36,827] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:27:36,827] [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_002531935.1	s__Rhizobium chutanense	100.0	2245	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.76	96.76	0.89	0.89	2	conclusive
GCF_014197615.1	s__Rhizobium esperanzae_A	93.6465	1695	2252	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	93.374	1800	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014198335.1	s__Rhizobium leguminosarum_N	92.0276	1652	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.95	99.93	0.95	0.91	10	-
GCF_002531725.1	s__Rhizobium sp002531725	91.8569	1831	2252	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	90.9559	1770	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.87	98.55	0.90	0.84	6	-
GCF_001664485.1	s__Rhizobium sp001664485	90.137	1825	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.08	96.02	0.91	0.83	8	-
GCF_000271845.1	s__Rhizobium leguminosarum_G	90.0765	1725	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531905.1	s__Rhizobium sp002531905	89.9364	1767	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.24	98.93	0.89	0.86	4	-
GCF_002531755.2	s__Rhizobium acidisoli	89.8606	1784	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.40	0.88	0.80	8	-
GCF_003985145.1	s__Rhizobium anhuiense	89.561	1719	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	-
GCF_003985155.1	s__Rhizobium vallis	89.4688	1741	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211285.1	s__Rhizobium sp002211285	89.3729	1601	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001657485.1	s__Rhizobium sp001657485	89.1006	1645	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.95	97.95	0.90	0.90	2	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	89.0493	1685	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.01	96.15	0.89	0.84	170	-
GCF_013087515.1	s__Rhizobium sophorae	88.9494	1661	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.85	95.49	0.87	0.83	6	-
GCF_900094625.1	s__Rhizobium aethiopicum	88.5455	1655	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.33	98.33	0.89	0.89	2	-
GCF_002211305.1	s__Rhizobium sp002211305	88.2883	1674	2252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.97	96.97	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:27:36,834] [INFO] GTDB search result was written to GCF_002531935.1_ASM253193v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:27:36,835] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:27:36,839] [INFO] DFAST_QC result json was written to GCF_002531935.1_ASM253193v1_genomic.fna/dqc_result.json
[2024-01-25 18:27:36,839] [INFO] DFAST_QC completed!
[2024-01-25 18:27:36,839] [INFO] Total running time: 0h2m16s