[2024-01-24 15:27:41,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgf37e5878-f32c-4cbf-9d43-15e114ecf50f/dqc_reference
[2024-01-24 15:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,883] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg39fda600-156b-4c24-8cc5-657c28edb4d2/GCF_007922615.2_ASM792261v2_genomic.fna.gz | prodigal -d GCF_007922615.2_ASM792261v2_genomic.fna/cds.fna -a GCF_007922615.2_ASM792261v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:58,390] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:58,390] [INFO] Task started: HMMsearch
[2024-01-24 15:27:58,390] [INFO] Running command: hmmsearch --tblout GCF_007922615.2_ASM792261v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf37e5878-f32c-4cbf-9d43-15e114ecf50f/dqc_reference/reference_markers.hmm GCF_007922615.2_ASM792261v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:58,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:58,676] [INFO] Found 6/6 markers.
[2024-01-24 15:27:58,718] [INFO] Query marker FASTA was written to GCF_007922615.2_ASM792261v2_genomic.fna/markers.fasta
[2024-01-24 15:27:58,718] [INFO] Task started: Blastn
[2024-01-24 15:27:58,718] [INFO] Running command: blastn -query GCF_007922615.2_ASM792261v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf37e5878-f32c-4cbf-9d43-15e114ecf50f/dqc_reference/reference_markers.fasta -out GCF_007922615.2_ASM792261v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:59,726] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:59,730] [INFO] Selected 19 target genomes.
[2024-01-24 15:27:59,731] [INFO] Target genome list was writen to GCF_007922615.2_ASM792261v2_genomic.fna/target_genomes.txt
[2024-01-24 15:27:59,739] [INFO] Task started: fastANI
[2024-01-24 15:27:59,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg39fda600-156b-4c24-8cc5-657c28edb4d2/GCF_007922615.2_ASM792261v2_genomic.fna.gz --refList GCF_007922615.2_ASM792261v2_genomic.fna/target_genomes.txt --output GCF_007922615.2_ASM792261v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:21,070] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:21,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf37e5878-f32c-4cbf-9d43-15e114ecf50f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:21,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf37e5878-f32c-4cbf-9d43-15e114ecf50f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:21,087] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:28:21,088] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:28:21,088] [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
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	81.9712	954	1618	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	81.6346	1003	1618	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	80.2287	863	1618	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	80.0807	848	1618	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	79.8844	735	1618	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	79.6545	674	1618	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	79.4793	634	1618	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	79.3802	675	1618	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	79.3743	624	1618	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	79.3534	662	1618	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	79.3515	623	1618	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	79.2735	685	1618	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.2085	644	1618	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	79.2008	672	1618	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	79.2007	604	1618	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.1468	665	1618	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	79.0026	616	1618	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.9974	533	1618	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.6637	528	1618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:21,090] [INFO] DFAST Taxonomy check result was written to GCF_007922615.2_ASM792261v2_genomic.fna/tc_result.tsv
[2024-01-24 15:28:21,090] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:21,090] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:21,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf37e5878-f32c-4cbf-9d43-15e114ecf50f/dqc_reference/checkm_data
[2024-01-24 15:28:21,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:21,135] [INFO] Task started: CheckM
[2024-01-24 15:28:21,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007922615.2_ASM792261v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007922615.2_ASM792261v2_genomic.fna/checkm_input GCF_007922615.2_ASM792261v2_genomic.fna/checkm_result
[2024-01-24 15:29:06,299] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:06,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:06,328] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:06,328] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:06,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007922615.2_ASM792261v2_genomic.fna/markers.fasta)
[2024-01-24 15:29:06,329] [INFO] Task started: Blastn
[2024-01-24 15:29:06,329] [INFO] Running command: blastn -query GCF_007922615.2_ASM792261v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf37e5878-f32c-4cbf-9d43-15e114ecf50f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007922615.2_ASM792261v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:08,394] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:08,399] [INFO] Selected 19 target genomes.
[2024-01-24 15:29:08,399] [INFO] Target genome list was writen to GCF_007922615.2_ASM792261v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:08,414] [INFO] Task started: fastANI
[2024-01-24 15:29:08,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg39fda600-156b-4c24-8cc5-657c28edb4d2/GCF_007922615.2_ASM792261v2_genomic.fna.gz --refList GCF_007922615.2_ASM792261v2_genomic.fna/target_genomes_gtdb.txt --output GCF_007922615.2_ASM792261v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:31,395] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:31,421] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:31,422] [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_007922615.2	s__Nitratireductor_D sp007922615	100.0	1618	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003015025.1	s__Nitratireductor_D sp003015025	81.9056	965	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_009742725.1	s__Nitratireductor_D arenosus	81.6135	1006	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	80.2284	863	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889605.1	s__Mesorhizobium_E oceanicum	80.0939	846	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	80.0692	698	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749525.1	s__Im94 sp009749525	79.9963	734	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Im94	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	79.8758	737	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	79.7193	722	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952465.1	s__Mesorhizobium sp003952465	79.5635	709	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_003952505.1	s__Mesorhizobium sp003952505	79.5544	705	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_002294995.1	s__Mesorhizobium sp002294995	79.4921	645	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	79.3848	683	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_000300335.1	s__Nitratireductor pacificus	79.3524	628	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830515.1	s__Mesorhizobium tianshanense	79.2199	661	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009812055.1	s__Chelativorans xinjiangense	79.1739	607	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503535.1	s__Mesorhizobium sp005503535	79.1656	663	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439515.1	s__Mesorhizobium sp006439515	79.1204	659	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.05	0.91	0.91	2	-
GCF_014863355.1	s__Aminobacter carboxidus	79.1109	652	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.38	98.38	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:31,424] [INFO] GTDB search result was written to GCF_007922615.2_ASM792261v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:31,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:31,431] [INFO] DFAST_QC result json was written to GCF_007922615.2_ASM792261v2_genomic.fna/dqc_result.json
[2024-01-24 15:29:31,431] [INFO] DFAST_QC completed!
[2024-01-24 15:29:31,431] [INFO] Total running time: 0h1m50s