[2024-01-24 15:18:27,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8d8d2d4-dc48-4173-afa8-1f7d6a00d08f/dqc_reference
[2024-01-24 15:18:29,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:29,201] [INFO] Task started: Prodigal
[2024-01-24 15:18:29,201] [INFO] Running command: gunzip -c /var/lib/cwl/stgee29ae9f-7567-4042-b7ae-18c976208b44/GCF_003258835.1_ASM325883v1_genomic.fna.gz | prodigal -d GCF_003258835.1_ASM325883v1_genomic.fna/cds.fna -a GCF_003258835.1_ASM325883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:43,895] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:43,895] [INFO] Task started: HMMsearch
[2024-01-24 15:18:43,895] [INFO] Running command: hmmsearch --tblout GCF_003258835.1_ASM325883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8d8d2d4-dc48-4173-afa8-1f7d6a00d08f/dqc_reference/reference_markers.hmm GCF_003258835.1_ASM325883v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:44,250] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:44,251] [INFO] Found 6/6 markers.
[2024-01-24 15:18:44,296] [INFO] Query marker FASTA was written to GCF_003258835.1_ASM325883v1_genomic.fna/markers.fasta
[2024-01-24 15:18:44,297] [INFO] Task started: Blastn
[2024-01-24 15:18:44,297] [INFO] Running command: blastn -query GCF_003258835.1_ASM325883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8d8d2d4-dc48-4173-afa8-1f7d6a00d08f/dqc_reference/reference_markers.fasta -out GCF_003258835.1_ASM325883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:45,386] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:45,390] [INFO] Selected 20 target genomes.
[2024-01-24 15:18:45,390] [INFO] Target genome list was writen to GCF_003258835.1_ASM325883v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:45,397] [INFO] Task started: fastANI
[2024-01-24 15:18:45,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgee29ae9f-7567-4042-b7ae-18c976208b44/GCF_003258835.1_ASM325883v1_genomic.fna.gz --refList GCF_003258835.1_ASM325883v1_genomic.fna/target_genomes.txt --output GCF_003258835.1_ASM325883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:06,894] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:06,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8d8d2d4-dc48-4173-afa8-1f7d6a00d08f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:06,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8d8d2d4-dc48-4173-afa8-1f7d6a00d08f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:06,911] [INFO] Found 20 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:19:06,911] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:06,911] [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
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	100.0	1654	1661	95	conclusive
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	99.9964	1648	1661	95	conclusive
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	99.9836	1634	1661	95	conclusive
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.3572	445	1661	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.2244	458	1661	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.2059	507	1661	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	78.1097	417	1661	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.0209	402	1661	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.9025	425	1661	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.8578	379	1661	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.8272	454	1661	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	77.7485	386	1661	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	77.7324	352	1661	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.6041	454	1661	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.5501	296	1661	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.3815	403	1661	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.285	437	1661	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	77.2327	384	1661	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.228	448	1661	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.945	256	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:06,914] [INFO] DFAST Taxonomy check result was written to GCF_003258835.1_ASM325883v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:06,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:06,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:06,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8d8d2d4-dc48-4173-afa8-1f7d6a00d08f/dqc_reference/checkm_data
[2024-01-24 15:19:06,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:06,975] [INFO] Task started: CheckM
[2024-01-24 15:19:06,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258835.1_ASM325883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258835.1_ASM325883v1_genomic.fna/checkm_input GCF_003258835.1_ASM325883v1_genomic.fna/checkm_result
[2024-01-24 15:19:50,678] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:50,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:50,701] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:50,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:50,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258835.1_ASM325883v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:50,702] [INFO] Task started: Blastn
[2024-01-24 15:19:50,702] [INFO] Running command: blastn -query GCF_003258835.1_ASM325883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8d8d2d4-dc48-4173-afa8-1f7d6a00d08f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258835.1_ASM325883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:52,814] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:52,817] [INFO] Selected 22 target genomes.
[2024-01-24 15:19:52,817] [INFO] Target genome list was writen to GCF_003258835.1_ASM325883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:52,834] [INFO] Task started: fastANI
[2024-01-24 15:19:52,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgee29ae9f-7567-4042-b7ae-18c976208b44/GCF_003258835.1_ASM325883v1_genomic.fna.gz --refList GCF_003258835.1_ASM325883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258835.1_ASM325883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:15,235] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:15,267] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:15,267] [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_003258835.1	s__Rhodobium orientis	100.0	1654	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	conclusive
GCA_002869065.1	s__Rhodobium sp002869065	79.4062	633	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	78.7108	513	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	78.6197	554	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_003610575.1	s__Stappia sp003610575	78.6141	515	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_001696535.1	s__Stappia indica	78.611	527	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	78.191	509	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_015904235.1	s__L22 sp015904235	78.186	501	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688515.1	s__Afifella pfennigii	78.0925	419	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	78.0905	465	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839525.1	s__Mongoliimonas rhizosphaerae	77.9003	423	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	77.8633	425	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	77.8613	544	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCF_013839445.1	s__Chthonobacter albigriseus	77.7556	385	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	77.751	444	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	77.7052	281	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	77.6325	450	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_006442795.1	s__Mesorhizobium sp006442795	77.6246	392	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	77.5708	435	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804325.1	s__Methylobacterium aquaticum_C	77.5099	419	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745635.1	s__Methylobacterium sp004745635	77.2373	449	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144885.1	s__Phreatobacter stygius	77.1754	392	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:15,269] [INFO] GTDB search result was written to GCF_003258835.1_ASM325883v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:15,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:15,276] [INFO] DFAST_QC result json was written to GCF_003258835.1_ASM325883v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:15,276] [INFO] DFAST_QC completed!
[2024-01-24 15:20:15,276] [INFO] Total running time: 0h1m48s