[2024-01-24 14:46:55,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,047] [INFO] DQC Reference Directory: /var/lib/cwl/stge02e576b-5b41-4c0e-af0a-3f27787bfcbe/dqc_reference
[2024-01-24 14:46:58,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,014] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg77d33fd3-65be-4cf8-97e2-4a0abf1b72cf/GCF_003970795.1_ASM397079v1_genomic.fna.gz | prodigal -d GCF_003970795.1_ASM397079v1_genomic.fna/cds.fna -a GCF_003970795.1_ASM397079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:13,734] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:13,734] [INFO] Task started: HMMsearch
[2024-01-24 14:47:13,735] [INFO] Running command: hmmsearch --tblout GCF_003970795.1_ASM397079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge02e576b-5b41-4c0e-af0a-3f27787bfcbe/dqc_reference/reference_markers.hmm GCF_003970795.1_ASM397079v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:14,027] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:14,028] [INFO] Found 6/6 markers.
[2024-01-24 14:47:14,074] [INFO] Query marker FASTA was written to GCF_003970795.1_ASM397079v1_genomic.fna/markers.fasta
[2024-01-24 14:47:14,075] [INFO] Task started: Blastn
[2024-01-24 14:47:14,075] [INFO] Running command: blastn -query GCF_003970795.1_ASM397079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge02e576b-5b41-4c0e-af0a-3f27787bfcbe/dqc_reference/reference_markers.fasta -out GCF_003970795.1_ASM397079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:15,205] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:15,210] [INFO] Selected 20 target genomes.
[2024-01-24 14:47:15,211] [INFO] Target genome list was writen to GCF_003970795.1_ASM397079v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:15,217] [INFO] Task started: fastANI
[2024-01-24 14:47:15,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d33fd3-65be-4cf8-97e2-4a0abf1b72cf/GCF_003970795.1_ASM397079v1_genomic.fna.gz --refList GCF_003970795.1_ASM397079v1_genomic.fna/target_genomes.txt --output GCF_003970795.1_ASM397079v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:37,881] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:37,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge02e576b-5b41-4c0e-af0a-3f27787bfcbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:37,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge02e576b-5b41-4c0e-af0a-3f27787bfcbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:37,898] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:37,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:37,898] [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 carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	100.0	1680	1691	95	conclusive
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	85.6208	1297	1691	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	81.3946	918	1691	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	79.7578	643	1691	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	79.7004	620	1691	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	79.6928	652	1691	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	79.5635	623	1691	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	79.5193	660	1691	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	79.5145	668	1691	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	79.5055	645	1691	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	79.4622	628	1691	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.29	690	1691	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.1682	637	1691	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	79.0622	477	1691	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9011	550	1691	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	78.7831	508	1691	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	78.4511	414	1691	95	below_threshold
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	77.6082	294	1691	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	76.6905	217	1691	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	76.0027	164	1691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:37,900] [INFO] DFAST Taxonomy check result was written to GCF_003970795.1_ASM397079v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:37,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:37,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:37,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge02e576b-5b41-4c0e-af0a-3f27787bfcbe/dqc_reference/checkm_data
[2024-01-24 14:47:37,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:37,957] [INFO] Task started: CheckM
[2024-01-24 14:47:37,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970795.1_ASM397079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970795.1_ASM397079v1_genomic.fna/checkm_input GCF_003970795.1_ASM397079v1_genomic.fna/checkm_result
[2024-01-24 14:48:28,458] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:28,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:28,478] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:28,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:28,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970795.1_ASM397079v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:28,480] [INFO] Task started: Blastn
[2024-01-24 14:48:28,480] [INFO] Running command: blastn -query GCF_003970795.1_ASM397079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge02e576b-5b41-4c0e-af0a-3f27787bfcbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970795.1_ASM397079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:30,705] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:30,710] [INFO] Selected 19 target genomes.
[2024-01-24 14:48:30,710] [INFO] Target genome list was writen to GCF_003970795.1_ASM397079v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:30,723] [INFO] Task started: fastANI
[2024-01-24 14:48:30,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d33fd3-65be-4cf8-97e2-4a0abf1b72cf/GCF_003970795.1_ASM397079v1_genomic.fna.gz --refList GCF_003970795.1_ASM397079v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970795.1_ASM397079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:51,702] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:51,721] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:51,721] [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_003970795.1	s__Mesorhizobium_E carbonis	100.0	1680	1691	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_014495845.1	s__Mesorhizobium_E sp014495845	85.6224	1297	1691	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	81.3999	917	1691	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_003577315.1	s__Aquamicrobium_A sp003577315	80.4166	564	1691	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_900177325.1	s__Mesorhizobium_A australicum_A	80.1425	782	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	80.1208	728	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	79.8927	632	1691	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	79.8728	694	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_003289965.1	s__Mesorhizobium atlanticum	79.7197	648	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016591715.1	s__Mesorhizobium sp016591715	79.6203	675	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180155.1	s__Aquamicrobium_A microcysteis	79.565	624	1691	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_000824805.1	s__Mesorhizobium sp000824805	79.5301	653	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	79.458	629	1691	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_008727715.1	s__Mesorhizobium terrae	79.399	647	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	-
GCA_017305925.1	s__JAFKJW01 sp017305925	79.3772	562	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	79.357	540	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCA_017306585.1	s__Mesorhizobium sp017306585	79.2852	620	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003934165.1	s__Pseudaminobacter arsenicus	78.6256	505	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056045.1	s__Paracoccus sp018056045	75.6362	101	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:51,723] [INFO] GTDB search result was written to GCF_003970795.1_ASM397079v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:51,723] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:51,728] [INFO] DFAST_QC result json was written to GCF_003970795.1_ASM397079v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:51,728] [INFO] DFAST_QC completed!
[2024-01-24 14:48:51,728] [INFO] Total running time: 0h1m57s