[2024-01-24 14:15:34,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,412] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg59216903-bb55-4fa6-bd1a-7f025dfe0c1c/dqc_reference
[2024-01-24 14:15:35,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,713] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cf33b8a-df6b-4d64-8c86-9a92e3d8cbec/GCF_004801285.1_ASM480128v1_genomic.fna.gz | prodigal -d GCF_004801285.1_ASM480128v1_genomic.fna/cds.fna -a GCF_004801285.1_ASM480128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:50,283] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:50,283] [INFO] Task started: HMMsearch
[2024-01-24 14:15:50,284] [INFO] Running command: hmmsearch --tblout GCF_004801285.1_ASM480128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59216903-bb55-4fa6-bd1a-7f025dfe0c1c/dqc_reference/reference_markers.hmm GCF_004801285.1_ASM480128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:50,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:50,614] [INFO] Found 6/6 markers.
[2024-01-24 14:15:50,657] [INFO] Query marker FASTA was written to GCF_004801285.1_ASM480128v1_genomic.fna/markers.fasta
[2024-01-24 14:15:50,657] [INFO] Task started: Blastn
[2024-01-24 14:15:50,657] [INFO] Running command: blastn -query GCF_004801285.1_ASM480128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59216903-bb55-4fa6-bd1a-7f025dfe0c1c/dqc_reference/reference_markers.fasta -out GCF_004801285.1_ASM480128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:51,768] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:51,773] [INFO] Selected 23 target genomes.
[2024-01-24 14:15:51,774] [INFO] Target genome list was writen to GCF_004801285.1_ASM480128v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:51,785] [INFO] Task started: fastANI
[2024-01-24 14:15:51,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cf33b8a-df6b-4d64-8c86-9a92e3d8cbec/GCF_004801285.1_ASM480128v1_genomic.fna.gz --refList GCF_004801285.1_ASM480128v1_genomic.fna/target_genomes.txt --output GCF_004801285.1_ASM480128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:22,103] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:22,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59216903-bb55-4fa6-bd1a-7f025dfe0c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:22,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59216903-bb55-4fa6-bd1a-7f025dfe0c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:22,121] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:16:22,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:22,122] [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
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	100.0	1532	1533	95	conclusive
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	82.2843	932	1533	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	82.2645	874	1533	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	82.2517	975	1533	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	82.1537	970	1533	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	82.081	940	1533	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	81.9003	922	1533	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	81.8769	972	1533	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	81.7246	968	1533	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	81.6944	860	1533	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	81.6255	970	1533	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	81.6027	875	1533	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	81.3681	822	1533	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	81.3131	893	1533	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	80.9974	823	1533	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	80.9636	690	1533	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	80.6391	813	1533	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	80.6298	812	1533	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.5482	786	1533	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	80.4276	650	1533	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.4849	659	1533	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.4723	661	1533	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.1519	602	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:22,123] [INFO] DFAST Taxonomy check result was written to GCF_004801285.1_ASM480128v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:22,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:22,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:22,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59216903-bb55-4fa6-bd1a-7f025dfe0c1c/dqc_reference/checkm_data
[2024-01-24 14:16:22,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:22,178] [INFO] Task started: CheckM
[2024-01-24 14:16:22,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801285.1_ASM480128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801285.1_ASM480128v1_genomic.fna/checkm_input GCF_004801285.1_ASM480128v1_genomic.fna/checkm_result
[2024-01-24 14:17:05,650] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:05,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:05,672] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:05,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:05,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801285.1_ASM480128v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:05,674] [INFO] Task started: Blastn
[2024-01-24 14:17:05,674] [INFO] Running command: blastn -query GCF_004801285.1_ASM480128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59216903-bb55-4fa6-bd1a-7f025dfe0c1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801285.1_ASM480128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:07,898] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:07,902] [INFO] Selected 20 target genomes.
[2024-01-24 14:17:07,902] [INFO] Target genome list was writen to GCF_004801285.1_ASM480128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:07,914] [INFO] Task started: fastANI
[2024-01-24 14:17:07,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cf33b8a-df6b-4d64-8c86-9a92e3d8cbec/GCF_004801285.1_ASM480128v1_genomic.fna.gz --refList GCF_004801285.1_ASM480128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801285.1_ASM480128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:32,181] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:32,207] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:32,207] [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_004801285.1	s__Mesorhizobium composti	100.0	1532	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	conclusive
GCA_017306545.1	s__Mesorhizobium sp017306545	88.9659	1117	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952505.1	s__Mesorhizobium sp003952505	82.4662	953	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_006442815.1	s__Mesorhizobium sp006442815	82.3204	969	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCA_001510895.1	s__Mesorhizobium loti_A	82.3153	968	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863365.1	s__Mesorhizobium tamadayense	82.279	933	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091085.1	s__Mesorhizobium sp019091085	82.274	984	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006440675.1	s__Mesorhizobium sp006440675	82.2361	951	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.39	95.73	0.91	0.84	9	-
GCA_004020545.1	s__Mesorhizobium sp004020545	82.1919	962	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_003952485.1	s__Mesorhizobium sp003952485	82.1754	962	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_016836705.1	s__Mesorhizobium caraganae	81.9154	919	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	-
GCA_017305835.1	s__RCIO01 sp017305835	81.2425	751	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427285.1	s__Mesorhizobium sp001427285	81.1032	757	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200015.1	s__Aminobacter niigataensis	81.0106	822	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_004363725.1	s__Mesorhizobium defluvii	80.9841	689	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.28	99.28	0.87	0.87	2	-
GCA_001724355.1	s__Aminobacter sp001724355	80.9008	651	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	80.6867	804	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	80.6522	382	1533	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_905339215.1	s__DUSC01 sp008933895	80.5315	701	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	80.5299	788	1533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:32,210] [INFO] GTDB search result was written to GCF_004801285.1_ASM480128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:32,210] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:32,215] [INFO] DFAST_QC result json was written to GCF_004801285.1_ASM480128v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:32,215] [INFO] DFAST_QC completed!
[2024-01-24 14:17:32,215] [INFO] Total running time: 0h1m58s