[2023-06-28 08:55:49,853] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:55:49,855] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:55:49,855] [INFO] DQC Reference Directory: /var/lib/cwl/stga1bcab99-f0f8-4f88-8353-4bdbbb75b699/dqc_reference
[2023-06-28 08:55:51,038] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:55:51,038] [INFO] Task started: Prodigal
[2023-06-28 08:55:51,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgc36f32c9-b723-42f1-9261-ecb7f963046e/GCA_002708825.1_ASM270882v1_genomic.fna.gz | prodigal -d GCA_002708825.1_ASM270882v1_genomic.fna/cds.fna -a GCA_002708825.1_ASM270882v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:56:05,354] [INFO] Task succeeded: Prodigal
[2023-06-28 08:56:05,355] [INFO] Task started: HMMsearch
[2023-06-28 08:56:05,355] [INFO] Running command: hmmsearch --tblout GCA_002708825.1_ASM270882v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1bcab99-f0f8-4f88-8353-4bdbbb75b699/dqc_reference/reference_markers.hmm GCA_002708825.1_ASM270882v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:56:05,583] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:56:05,584] [INFO] Found 6/6 markers.
[2023-06-28 08:56:05,621] [INFO] Query marker FASTA was written to GCA_002708825.1_ASM270882v1_genomic.fna/markers.fasta
[2023-06-28 08:56:05,621] [INFO] Task started: Blastn
[2023-06-28 08:56:05,621] [INFO] Running command: blastn -query GCA_002708825.1_ASM270882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1bcab99-f0f8-4f88-8353-4bdbbb75b699/dqc_reference/reference_markers.fasta -out GCA_002708825.1_ASM270882v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:56:06,681] [INFO] Task succeeded: Blastn
[2023-06-28 08:56:06,684] [INFO] Selected 23 target genomes.
[2023-06-28 08:56:06,685] [INFO] Target genome list was writen to GCA_002708825.1_ASM270882v1_genomic.fna/target_genomes.txt
[2023-06-28 08:56:06,687] [INFO] Task started: fastANI
[2023-06-28 08:56:06,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgc36f32c9-b723-42f1-9261-ecb7f963046e/GCA_002708825.1_ASM270882v1_genomic.fna.gz --refList GCA_002708825.1_ASM270882v1_genomic.fna/target_genomes.txt --output GCA_002708825.1_ASM270882v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:56:27,216] [INFO] Task succeeded: fastANI
[2023-06-28 08:56:27,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1bcab99-f0f8-4f88-8353-4bdbbb75b699/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:56:27,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1bcab99-f0f8-4f88-8353-4bdbbb75b699/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:56:27,234] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:56:27,234] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 08:56:27,234] [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
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	83.1029	979	1541	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.5514	570	1541	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	79.0663	500	1541	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	79.0461	487	1541	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.0153	577	1541	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	78.8765	503	1541	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	78.8589	486	1541	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	78.7811	491	1541	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	78.6842	427	1541	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.6556	443	1541	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	78.6042	508	1541	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.5719	483	1541	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	78.5482	454	1541	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	78.5422	419	1541	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	78.5006	503	1541	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	78.37	449	1541	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	78.3471	485	1541	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.2478	358	1541	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.2382	359	1541	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	78.0879	344	1541	95	below_threshold
Martelella lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	77.8835	294	1541	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.5895	283	1541	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.9994	194	1541	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 08:56:27,236] [INFO] DFAST Taxonomy check result was written to GCA_002708825.1_ASM270882v1_genomic.fna/tc_result.tsv
[2023-06-28 08:56:27,236] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:56:27,237] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:56:27,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1bcab99-f0f8-4f88-8353-4bdbbb75b699/dqc_reference/checkm_data
[2023-06-28 08:56:27,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:56:27,280] [INFO] Task started: CheckM
[2023-06-28 08:56:27,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708825.1_ASM270882v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708825.1_ASM270882v1_genomic.fna/checkm_input GCA_002708825.1_ASM270882v1_genomic.fna/checkm_result
[2023-06-28 08:57:20,427] [INFO] Task succeeded: CheckM
[2023-06-28 08:57:20,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:57:20,444] [INFO] ===== Completeness check finished =====
[2023-06-28 08:57:20,444] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:57:20,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708825.1_ASM270882v1_genomic.fna/markers.fasta)
[2023-06-28 08:57:20,445] [INFO] Task started: Blastn
[2023-06-28 08:57:20,445] [INFO] Running command: blastn -query GCA_002708825.1_ASM270882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1bcab99-f0f8-4f88-8353-4bdbbb75b699/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708825.1_ASM270882v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:57:22,568] [INFO] Task succeeded: Blastn
[2023-06-28 08:57:22,571] [INFO] Selected 22 target genomes.
[2023-06-28 08:57:22,571] [INFO] Target genome list was writen to GCA_002708825.1_ASM270882v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:57:22,578] [INFO] Task started: fastANI
[2023-06-28 08:57:22,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgc36f32c9-b723-42f1-9261-ecb7f963046e/GCA_002708825.1_ASM270882v1_genomic.fna.gz --refList GCA_002708825.1_ASM270882v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708825.1_ASM270882v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:57:42,152] [INFO] Task succeeded: fastANI
[2023-06-28 08:57:42,169] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:57:42,169] [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
GCA_002708825.1	s__Zhengella sp002708825	100.0	1535	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	99.96	99.96	0.93	0.93	2	conclusive
GCF_002727065.1	s__Zhengella mangrovi	83.1029	979	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	79.0	579	1541	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_014860725.1	s__Aquamicrobium_A sp014860725	78.9413	295	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	78.8863	509	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	78.8676	504	1541	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	78.8217	537	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306545.1	s__Mesorhizobium sp017306545	78.7967	470	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	78.7724	507	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177325.1	s__Mesorhizobium_A australicum_A	78.7227	516	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	78.7167	446	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCA_018823835.1	s__RCIZ01 sp018823835	78.6339	469	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_001889605.1	s__Mesorhizobium_E oceanicum	78.588	510	1541	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_007922615.2	s__Nitratireductor_D sp007922615	78.5831	514	1541	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_016711085.1	s__JADJTR01 sp016711085	78.5174	423	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JADJTR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	78.5122	492	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_003666685.1	s__RCIZ01 sp003666685	78.4229	452	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756615.1	s__DUSC01 sp016756615	78.2674	509	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	98.60	98.60	0.90	0.90	2	-
GCF_003149475.2	s__Roseitalea stylonematis	78.1607	375	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	-
GCF_000300515.1	s__Nitratireductor indicus	78.0987	343	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003046185.1	s__Phreatobacter oligotrophus	77.6094	282	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603335.1	s__Alpha-05 sp001603335	76.8769	86	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:57:42,171] [INFO] GTDB search result was written to GCA_002708825.1_ASM270882v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:57:42,172] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:57:42,182] [INFO] DFAST_QC result json was written to GCA_002708825.1_ASM270882v1_genomic.fna/dqc_result.json
[2023-06-28 08:57:42,182] [INFO] DFAST_QC completed!
[2023-06-28 08:57:42,182] [INFO] Total running time: 0h1m52s