[2024-01-24 12:47:48,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:48,996] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:48,996] [INFO] DQC Reference Directory: /var/lib/cwl/stga45bc43d-5d77-456c-9fa8-13a8f7eb242e/dqc_reference
[2024-01-24 12:47:50,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,335] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,335] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cea8b47-7ed4-407a-857c-a106bb2f6732/GCF_010993735.1_ASM1099373v1_genomic.fna.gz | prodigal -d GCF_010993735.1_ASM1099373v1_genomic.fna/cds.fna -a GCF_010993735.1_ASM1099373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:07,678] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:07,679] [INFO] Task started: HMMsearch
[2024-01-24 12:48:07,679] [INFO] Running command: hmmsearch --tblout GCF_010993735.1_ASM1099373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga45bc43d-5d77-456c-9fa8-13a8f7eb242e/dqc_reference/reference_markers.hmm GCF_010993735.1_ASM1099373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:07,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:07,997] [INFO] Found 6/6 markers.
[2024-01-24 12:48:08,049] [INFO] Query marker FASTA was written to GCF_010993735.1_ASM1099373v1_genomic.fna/markers.fasta
[2024-01-24 12:48:08,050] [INFO] Task started: Blastn
[2024-01-24 12:48:08,050] [INFO] Running command: blastn -query GCF_010993735.1_ASM1099373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga45bc43d-5d77-456c-9fa8-13a8f7eb242e/dqc_reference/reference_markers.fasta -out GCF_010993735.1_ASM1099373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:09,167] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:09,171] [INFO] Selected 14 target genomes.
[2024-01-24 12:48:09,171] [INFO] Target genome list was writen to GCF_010993735.1_ASM1099373v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:09,174] [INFO] Task started: fastANI
[2024-01-24 12:48:09,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cea8b47-7ed4-407a-857c-a106bb2f6732/GCF_010993735.1_ASM1099373v1_genomic.fna.gz --refList GCF_010993735.1_ASM1099373v1_genomic.fna/target_genomes.txt --output GCF_010993735.1_ASM1099373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:26,310] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:26,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga45bc43d-5d77-456c-9fa8-13a8f7eb242e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:26,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga45bc43d-5d77-456c-9fa8-13a8f7eb242e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:26,322] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:26,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:26,322] [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
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	100.0	1882	1883	95	conclusive
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	94.2518	1430	1883	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	82.5603	863	1883	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	80.1444	752	1883	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	80.1108	672	1883	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	79.53	586	1883	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.2236	638	1883	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	79.0276	641	1883	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.6189	554	1883	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.5898	597	1883	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	78.5405	473	1883	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	78.5356	589	1883	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.4628	581	1883	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.3948	473	1883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:26,325] [INFO] DFAST Taxonomy check result was written to GCF_010993735.1_ASM1099373v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:26,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:26,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:26,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga45bc43d-5d77-456c-9fa8-13a8f7eb242e/dqc_reference/checkm_data
[2024-01-24 12:48:26,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:26,379] [INFO] Task started: CheckM
[2024-01-24 12:48:26,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010993735.1_ASM1099373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010993735.1_ASM1099373v1_genomic.fna/checkm_input GCF_010993735.1_ASM1099373v1_genomic.fna/checkm_result
[2024-01-24 12:49:15,523] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:15,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:15,547] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:15,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:15,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010993735.1_ASM1099373v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:15,548] [INFO] Task started: Blastn
[2024-01-24 12:49:15,548] [INFO] Running command: blastn -query GCF_010993735.1_ASM1099373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga45bc43d-5d77-456c-9fa8-13a8f7eb242e/dqc_reference/reference_markers_gtdb.fasta -out GCF_010993735.1_ASM1099373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:17,755] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:17,759] [INFO] Selected 17 target genomes.
[2024-01-24 12:49:17,759] [INFO] Target genome list was writen to GCF_010993735.1_ASM1099373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:17,767] [INFO] Task started: fastANI
[2024-01-24 12:49:17,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cea8b47-7ed4-407a-857c-a106bb2f6732/GCF_010993735.1_ASM1099373v1_genomic.fna.gz --refList GCF_010993735.1_ASM1099373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010993735.1_ASM1099373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:34,964] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:34,985] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:34,985] [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_010993735.1	s__Chelativorans alearense	100.0	1882	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009812055.1	s__Chelativorans xinjiangense	94.2241	1432	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	80.0737	676	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	79.9606	547	1883	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_017305835.1	s__RCIO01 sp017305835	79.7795	645	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	79.507	590	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	79.1707	656	1883	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_018823835.1	s__RCIZ01 sp018823835	79.113	567	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_017255295.1	s__Nitratireductor aquimarinus	79.0479	581	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	98.42	98.07	0.93	0.92	7	-
GCF_011317445.1	s__Chelativorans multitrophicus	78.982	546	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	99.92	99.90	0.98	0.98	3	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	78.7615	651	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824805.1	s__Mesorhizobium sp000824805	78.7526	610	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518985.1	s__Chelativorans sp000518985	78.5622	510	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300515.1	s__Nitratireductor indicus	78.5319	474	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008180155.1	s__Aquamicrobium_A microcysteis	78.5087	571	1883	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_017306585.1	s__Mesorhizobium sp017306585	78.3545	556	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603335.1	s__Alpha-05 sp001603335	76.1609	98	1883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:34,987] [INFO] GTDB search result was written to GCF_010993735.1_ASM1099373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:34,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:34,991] [INFO] DFAST_QC result json was written to GCF_010993735.1_ASM1099373v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:34,991] [INFO] DFAST_QC completed!
[2024-01-24 12:49:34,991] [INFO] Total running time: 0h1m46s