[2024-01-24 11:44:23,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b5a5d19-5fdb-45de-b5e1-520a33d53d15/dqc_reference
[2024-01-24 11:44:26,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,341] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg424536ef-264a-420d-adaa-d8f94fa74503/GCF_017873095.1_ASM1787309v1_genomic.fna.gz | prodigal -d GCF_017873095.1_ASM1787309v1_genomic.fna/cds.fna -a GCF_017873095.1_ASM1787309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:42,138] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:42,139] [INFO] Task started: HMMsearch
[2024-01-24 11:44:42,139] [INFO] Running command: hmmsearch --tblout GCF_017873095.1_ASM1787309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b5a5d19-5fdb-45de-b5e1-520a33d53d15/dqc_reference/reference_markers.hmm GCF_017873095.1_ASM1787309v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:42,437] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:42,439] [INFO] Found 6/6 markers.
[2024-01-24 11:44:42,484] [INFO] Query marker FASTA was written to GCF_017873095.1_ASM1787309v1_genomic.fna/markers.fasta
[2024-01-24 11:44:42,485] [INFO] Task started: Blastn
[2024-01-24 11:44:42,485] [INFO] Running command: blastn -query GCF_017873095.1_ASM1787309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b5a5d19-5fdb-45de-b5e1-520a33d53d15/dqc_reference/reference_markers.fasta -out GCF_017873095.1_ASM1787309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:43,530] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:43,534] [INFO] Selected 23 target genomes.
[2024-01-24 11:44:43,534] [INFO] Target genome list was writen to GCF_017873095.1_ASM1787309v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:43,542] [INFO] Task started: fastANI
[2024-01-24 11:44:43,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg424536ef-264a-420d-adaa-d8f94fa74503/GCF_017873095.1_ASM1787309v1_genomic.fna.gz --refList GCF_017873095.1_ASM1787309v1_genomic.fna/target_genomes.txt --output GCF_017873095.1_ASM1787309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:07,771] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:07,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b5a5d19-5fdb-45de-b5e1-520a33d53d15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:07,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b5a5d19-5fdb-45de-b5e1-520a33d53d15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:07,789] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:07,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:07,789] [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 halophytocola	strain=DSM 21600	GCA_017873095.1	735519	735519	type	True	100.0	1769	1770	95	conclusive
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	80.7204	839	1770	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	80.1182	729	1770	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.867	731	1770	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	79.8056	698	1770	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.8006	638	1770	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.797	687	1770	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	79.7693	679	1770	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	79.7391	696	1770	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.7283	677	1770	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	79.7263	687	1770	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	79.7123	722	1770	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	79.6953	694	1770	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	79.6395	663	1770	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.6173	611	1770	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	79.6048	621	1770	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	79.5999	704	1770	95	below_threshold
Rhizobium daejeonense	strain=CCBAU10050	GCA_011045155.1	240521	240521	type	True	79.5601	665	1770	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	79.5515	706	1770	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	79.5183	693	1770	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	79.403	678	1770	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	79.3748	666	1770	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.0141	600	1770	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,791] [INFO] DFAST Taxonomy check result was written to GCF_017873095.1_ASM1787309v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:07,792] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:07,792] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:07,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b5a5d19-5fdb-45de-b5e1-520a33d53d15/dqc_reference/checkm_data
[2024-01-24 11:45:07,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:07,847] [INFO] Task started: CheckM
[2024-01-24 11:45:07,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873095.1_ASM1787309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873095.1_ASM1787309v1_genomic.fna/checkm_input GCF_017873095.1_ASM1787309v1_genomic.fna/checkm_result
[2024-01-24 11:45:54,798] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:54,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:54,821] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:54,822] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:54,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873095.1_ASM1787309v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:54,823] [INFO] Task started: Blastn
[2024-01-24 11:45:54,823] [INFO] Running command: blastn -query GCF_017873095.1_ASM1787309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b5a5d19-5fdb-45de-b5e1-520a33d53d15/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873095.1_ASM1787309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:56,922] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:56,927] [INFO] Selected 23 target genomes.
[2024-01-24 11:45:56,927] [INFO] Target genome list was writen to GCF_017873095.1_ASM1787309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:56,945] [INFO] Task started: fastANI
[2024-01-24 11:45:56,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg424536ef-264a-420d-adaa-d8f94fa74503/GCF_017873095.1_ASM1787309v1_genomic.fna.gz --refList GCF_017873095.1_ASM1787309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873095.1_ASM1787309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:21,098] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:21,120] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:21,120] [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_017873095.1	s__Allorhizobium halophytocola	100.0	1769	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002796995.1	s__Allorhizobium sp002796995	80.8855	854	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCF_000518785.1	s__Allorhizobium selenitireducens	80.7237	838	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900492205.1	s__Allorhizobium naphthalenivorans_A	80.7095	815	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.27	95.27	0.88	0.88	2	-
GCF_012276985.1	s__Allorhizobium sp012276985	80.355	841	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205195.1	s__Allorhizobium wuzhouense	80.1151	729	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.59	97.59	0.92	0.92	2	-
GCA_900470155.1	s__Allorhizobium sp900470155	80.0993	725	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912135.1	s__Allorhizobium rosettiformans	80.0448	722	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCA_900466005.1	s__Allorhizobium sp900466005	79.8407	686	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCA_900471605.1	s__Neorhizobium sp900471605	79.8314	770	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCA_900473805.1	s__Allorhizobium sp900473805	79.8275	697	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.45	97.28	0.98	0.92	6	-
GCF_001664485.1	s__Rhizobium sp001664485	79.8156	702	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.08	96.02	0.91	0.83	8	-
GCF_011046245.1	s__Rhizobium_A pseudoryzae	79.7998	698	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	79.778	707	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877135.1	s__Rhizobium_A galegae_A	79.7324	688	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732195.1	s__Neorhizobium vignae	79.7312	719	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014126615.1	s__Allorhizobium thiooxidans	79.7223	687	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300855.1	s__Allorhizobium albertimagni	79.7129	731	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337715.1	s__Allorhizobium lividum	79.6881	695	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000722615.1	s__Pseudorhizobium pelagicum	79.6844	655	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	97.63	97.12	0.87	0.82	8	-
GCF_014280875.1	s__Allorhizobium daejeonense	79.6351	664	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013087515.1	s__Rhizobium sophorae	79.5663	703	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.85	95.49	0.87	0.83	6	-
GCF_017357385.1	s__Rhizobium sp017357385	79.5249	683	1770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:21,122] [INFO] GTDB search result was written to GCF_017873095.1_ASM1787309v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:21,123] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:21,128] [INFO] DFAST_QC result json was written to GCF_017873095.1_ASM1787309v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:21,128] [INFO] DFAST_QC completed!
[2024-01-24 11:46:21,128] [INFO] Total running time: 0h1m58s