[2023-06-28 10:45:53,990] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:45:54,000] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:45:54,000] [INFO] DQC Reference Directory: /var/lib/cwl/stga296f7c7-6440-4d44-bcde-8e9f5a56dc3c/dqc_reference
[2023-06-28 10:45:55,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:45:55,585] [INFO] Task started: Prodigal
[2023-06-28 10:45:55,586] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9c3ce88-1958-4105-a82e-1d9855c8cc3d/GCA_017641265.1_ASM1764126v1_genomic.fna.gz | prodigal -d GCA_017641265.1_ASM1764126v1_genomic.fna/cds.fna -a GCA_017641265.1_ASM1764126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:46:07,533] [INFO] Task succeeded: Prodigal
[2023-06-28 10:46:07,533] [INFO] Task started: HMMsearch
[2023-06-28 10:46:07,533] [INFO] Running command: hmmsearch --tblout GCA_017641265.1_ASM1764126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga296f7c7-6440-4d44-bcde-8e9f5a56dc3c/dqc_reference/reference_markers.hmm GCA_017641265.1_ASM1764126v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:46:07,824] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:46:07,825] [INFO] Found 6/6 markers.
[2023-06-28 10:46:07,858] [INFO] Query marker FASTA was written to GCA_017641265.1_ASM1764126v1_genomic.fna/markers.fasta
[2023-06-28 10:46:07,859] [INFO] Task started: Blastn
[2023-06-28 10:46:07,859] [INFO] Running command: blastn -query GCA_017641265.1_ASM1764126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga296f7c7-6440-4d44-bcde-8e9f5a56dc3c/dqc_reference/reference_markers.fasta -out GCA_017641265.1_ASM1764126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:46:08,989] [INFO] Task succeeded: Blastn
[2023-06-28 10:46:08,993] [INFO] Selected 28 target genomes.
[2023-06-28 10:46:08,994] [INFO] Target genome list was writen to GCA_017641265.1_ASM1764126v1_genomic.fna/target_genomes.txt
[2023-06-28 10:46:08,996] [INFO] Task started: fastANI
[2023-06-28 10:46:08,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9c3ce88-1958-4105-a82e-1d9855c8cc3d/GCA_017641265.1_ASM1764126v1_genomic.fna.gz --refList GCA_017641265.1_ASM1764126v1_genomic.fna/target_genomes.txt --output GCA_017641265.1_ASM1764126v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:46:41,743] [INFO] Task succeeded: fastANI
[2023-06-28 10:46:41,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga296f7c7-6440-4d44-bcde-8e9f5a56dc3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:46:41,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga296f7c7-6440-4d44-bcde-8e9f5a56dc3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:46:41,764] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:46:41,764] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:46:41,764] [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
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	78.7383	444	1229	95	below_threshold
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	78.5372	407	1229	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.2201	443	1229	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	78.1399	389	1229	95	below_threshold
Oricola cellulosilytica	strain=JCM 19534	GCA_019966575.1	1429082	1429082	type	True	78.1095	325	1229	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.1014	370	1229	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	78.1011	454	1229	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	78.0253	424	1229	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	78.016	420	1229	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	77.9659	378	1229	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.9469	401	1229	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	77.9336	367	1229	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	77.9134	405	1229	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	77.9075	398	1229	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	77.843	394	1229	95	below_threshold
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	77.7047	305	1229	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	77.6867	384	1229	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	77.6589	410	1229	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	77.6114	330	1229	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.3599	315	1229	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.3599	315	1229	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	77.3513	286	1229	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	77.3159	325	1229	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	77.3029	269	1229	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	77.2567	244	1229	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	76.7285	136	1229	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.7248	256	1229	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	76.4471	185	1229	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:46:41,766] [INFO] DFAST Taxonomy check result was written to GCA_017641265.1_ASM1764126v1_genomic.fna/tc_result.tsv
[2023-06-28 10:46:41,768] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:46:41,768] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:46:41,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga296f7c7-6440-4d44-bcde-8e9f5a56dc3c/dqc_reference/checkm_data
[2023-06-28 10:46:41,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:46:41,810] [INFO] Task started: CheckM
[2023-06-28 10:46:41,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017641265.1_ASM1764126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017641265.1_ASM1764126v1_genomic.fna/checkm_input GCA_017641265.1_ASM1764126v1_genomic.fna/checkm_result
[2023-06-28 10:47:23,149] [INFO] Task succeeded: CheckM
[2023-06-28 10:47:23,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:47:23,184] [INFO] ===== Completeness check finished =====
[2023-06-28 10:47:23,185] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:47:23,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017641265.1_ASM1764126v1_genomic.fna/markers.fasta)
[2023-06-28 10:47:23,185] [INFO] Task started: Blastn
[2023-06-28 10:47:23,186] [INFO] Running command: blastn -query GCA_017641265.1_ASM1764126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga296f7c7-6440-4d44-bcde-8e9f5a56dc3c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017641265.1_ASM1764126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:25,228] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:25,233] [INFO] Selected 14 target genomes.
[2023-06-28 10:47:25,233] [INFO] Target genome list was writen to GCA_017641265.1_ASM1764126v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:47:25,240] [INFO] Task started: fastANI
[2023-06-28 10:47:25,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9c3ce88-1958-4105-a82e-1d9855c8cc3d/GCA_017641265.1_ASM1764126v1_genomic.fna.gz --refList GCA_017641265.1_ASM1764126v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017641265.1_ASM1764126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:47:41,007] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:41,025] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:47:41,025] [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_003149475.2	s__Roseitalea stylonematis	98.969	1142	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	conclusive
GCA_017642895.1	s__Roseitalea sp017642895	87.3759	939	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	99.99	99.99	1.00	1.00	3	-
GCF_004331955.1	s__Roseitalea porphyridii	83.3875	834	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	78.9727	529	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698425.1	s__Oricola sp002698425	78.7565	512	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	78.5064	365	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706335.1	s__Oricola sp002706335	78.2417	451	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952485.1	s__Mesorhizobium sp003952485	78.0924	436	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCA_004020545.1	s__Mesorhizobium sp004020545	77.9474	415	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_013520985.1	s__Mesorhizobium sp013520985	77.9068	405	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911015.1	s__Aliihoeflea sp012911015	77.8186	351	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197615.1	s__Rhizobium esperanzae_A	77.4232	309	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595955.1	s__Mesorhizobium_D sp014595955	77.3705	315	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003963455.1	s__Mesorhizobium sp003963455	77.0858	299	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:47:41,028] [INFO] GTDB search result was written to GCA_017641265.1_ASM1764126v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:47:41,028] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:47:41,033] [INFO] DFAST_QC result json was written to GCA_017641265.1_ASM1764126v1_genomic.fna/dqc_result.json
[2023-06-28 10:47:41,033] [INFO] DFAST_QC completed!
[2023-06-28 10:47:41,033] [INFO] Total running time: 0h1m47s