[2024-01-24 13:49:40,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,992] [INFO] DQC Reference Directory: /var/lib/cwl/stgb58590e3-ba25-40cf-8c82-733c30aec1a7/dqc_reference
[2024-01-24 13:49:42,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,339] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,339] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4aefe9b-7893-456e-b20c-2769a94a3208/GCF_014495845.1_ASM1449584v1_genomic.fna.gz | prodigal -d GCF_014495845.1_ASM1449584v1_genomic.fna/cds.fna -a GCF_014495845.1_ASM1449584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:59,602] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:59,602] [INFO] Task started: HMMsearch
[2024-01-24 13:49:59,603] [INFO] Running command: hmmsearch --tblout GCF_014495845.1_ASM1449584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb58590e3-ba25-40cf-8c82-733c30aec1a7/dqc_reference/reference_markers.hmm GCF_014495845.1_ASM1449584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:59,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:59,893] [INFO] Found 6/6 markers.
[2024-01-24 13:49:59,943] [INFO] Query marker FASTA was written to GCF_014495845.1_ASM1449584v1_genomic.fna/markers.fasta
[2024-01-24 13:49:59,943] [INFO] Task started: Blastn
[2024-01-24 13:49:59,944] [INFO] Running command: blastn -query GCF_014495845.1_ASM1449584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb58590e3-ba25-40cf-8c82-733c30aec1a7/dqc_reference/reference_markers.fasta -out GCF_014495845.1_ASM1449584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:00,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:00,993] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:00,994] [INFO] Target genome list was writen to GCF_014495845.1_ASM1449584v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:01,009] [INFO] Task started: fastANI
[2024-01-24 13:50:01,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4aefe9b-7893-456e-b20c-2769a94a3208/GCF_014495845.1_ASM1449584v1_genomic.fna.gz --refList GCF_014495845.1_ASM1449584v1_genomic.fna/target_genomes.txt --output GCF_014495845.1_ASM1449584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:23,720] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:23,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb58590e3-ba25-40cf-8c82-733c30aec1a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:23,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb58590e3-ba25-40cf-8c82-733c30aec1a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:23,735] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:23,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:23,736] [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
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	100.0	2035	2036	95	conclusive
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	85.5225	1289	2036	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	81.9864	1033	2036	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	80.1661	733	2036	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	80.0036	692	2036	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	79.9123	710	2036	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.9013	800	2036	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	79.7279	766	2036	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	79.681	742	2036	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	79.6062	692	2036	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.595	717	2036	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.5745	778	2036	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	79.5639	729	2036	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.5423	671	2036	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.4757	770	2036	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	79.3804	658	2036	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	79.2492	538	2036	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.0739	473	2036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:23,740] [INFO] DFAST Taxonomy check result was written to GCF_014495845.1_ASM1449584v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:23,741] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:23,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:23,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb58590e3-ba25-40cf-8c82-733c30aec1a7/dqc_reference/checkm_data
[2024-01-24 13:50:23,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:23,799] [INFO] Task started: CheckM
[2024-01-24 13:50:23,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014495845.1_ASM1449584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014495845.1_ASM1449584v1_genomic.fna/checkm_input GCF_014495845.1_ASM1449584v1_genomic.fna/checkm_result
[2024-01-24 13:51:29,521] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:29,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:29,575] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:29,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:29,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014495845.1_ASM1449584v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:29,576] [INFO] Task started: Blastn
[2024-01-24 13:51:29,576] [INFO] Running command: blastn -query GCF_014495845.1_ASM1449584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb58590e3-ba25-40cf-8c82-733c30aec1a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014495845.1_ASM1449584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:31,381] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:31,385] [INFO] Selected 16 target genomes.
[2024-01-24 13:51:31,385] [INFO] Target genome list was writen to GCF_014495845.1_ASM1449584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:31,428] [INFO] Task started: fastANI
[2024-01-24 13:51:31,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4aefe9b-7893-456e-b20c-2769a94a3208/GCF_014495845.1_ASM1449584v1_genomic.fna.gz --refList GCF_014495845.1_ASM1449584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014495845.1_ASM1449584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:50,722] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:50,735] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:50,735] [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_014495845.1	s__Mesorhizobium_E sp014495845	100.0	2034	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003970795.1	s__Mesorhizobium_E carbonis	85.5293	1288	2036	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	81.9809	1033	2036	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	80.8956	802	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	80.8762	658	2036	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	80.5607	860	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_014206975.1	s__Aminobacter aganoensis	80.1656	735	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	-
GCF_003952505.1	s__Mesorhizobium sp003952505	80.0702	751	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_014200015.1	s__Aminobacter niigataensis	80.0119	691	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCA_004963905.1	s__Mesorhizobium sp004963905	79.9655	804	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	79.8722	780	2036	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_003015025.1	s__Nitratireductor_D sp003015025	79.821	804	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCA_017305925.1	s__JAFKJW01 sp017305925	79.7671	643	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016836705.1	s__Mesorhizobium caraganae	79.6662	743	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	79.5987	693	2036	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_012911015.1	s__Aliihoeflea sp012911015	79.2623	615	2036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:50,737] [INFO] GTDB search result was written to GCF_014495845.1_ASM1449584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:50,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:50,741] [INFO] DFAST_QC result json was written to GCF_014495845.1_ASM1449584v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:50,741] [INFO] DFAST_QC completed!
[2024-01-24 13:51:50,741] [INFO] Total running time: 0h2m10s