[2023-06-28 10:00:49,843] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:00:49,850] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:00:49,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg9daff234-e7a9-466e-b5bb-a568943d5347/dqc_reference
[2023-06-28 10:00:51,468] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:00:51,469] [INFO] Task started: Prodigal
[2023-06-28 10:00:51,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f71c2e2-7939-4e56-8465-448093f99d8b/GCA_017642845.1_ASM1764284v1_genomic.fna.gz | prodigal -d GCA_017642845.1_ASM1764284v1_genomic.fna/cds.fna -a GCA_017642845.1_ASM1764284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:01:01,139] [INFO] Task succeeded: Prodigal
[2023-06-28 10:01:01,140] [INFO] Task started: HMMsearch
[2023-06-28 10:01:01,140] [INFO] Running command: hmmsearch --tblout GCA_017642845.1_ASM1764284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9daff234-e7a9-466e-b5bb-a568943d5347/dqc_reference/reference_markers.hmm GCA_017642845.1_ASM1764284v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:01:01,408] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:01:01,410] [INFO] Found 6/6 markers.
[2023-06-28 10:01:01,446] [INFO] Query marker FASTA was written to GCA_017642845.1_ASM1764284v1_genomic.fna/markers.fasta
[2023-06-28 10:01:01,447] [INFO] Task started: Blastn
[2023-06-28 10:01:01,447] [INFO] Running command: blastn -query GCA_017642845.1_ASM1764284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9daff234-e7a9-466e-b5bb-a568943d5347/dqc_reference/reference_markers.fasta -out GCA_017642845.1_ASM1764284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:02,370] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:02,374] [INFO] Selected 18 target genomes.
[2023-06-28 10:01:02,375] [INFO] Target genome list was writen to GCA_017642845.1_ASM1764284v1_genomic.fna/target_genomes.txt
[2023-06-28 10:01:02,377] [INFO] Task started: fastANI
[2023-06-28 10:01:02,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f71c2e2-7939-4e56-8465-448093f99d8b/GCA_017642845.1_ASM1764284v1_genomic.fna.gz --refList GCA_017642845.1_ASM1764284v1_genomic.fna/target_genomes.txt --output GCA_017642845.1_ASM1764284v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:01:17,583] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:17,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9daff234-e7a9-466e-b5bb-a568943d5347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:01:17,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9daff234-e7a9-466e-b5bb-a568943d5347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:01:17,603] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:01:17,604] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:01:17,604] [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
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	82.4134	765	1137	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.8843	552	1137	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.5365	533	1137	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.9766	308	1137	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.9929	153	1137	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.8647	146	1137	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.8451	183	1137	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.8309	198	1137	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.8182	179	1137	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	76.8035	133	1137	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	76.6248	128	1137	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	76.6024	173	1137	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	76.5141	159	1137	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.4886	136	1137	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	76.426	162	1137	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.4172	133	1137	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.4141	115	1137	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	76.3535	95	1137	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:01:17,607] [INFO] DFAST Taxonomy check result was written to GCA_017642845.1_ASM1764284v1_genomic.fna/tc_result.tsv
[2023-06-28 10:01:17,608] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:01:17,608] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:01:17,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9daff234-e7a9-466e-b5bb-a568943d5347/dqc_reference/checkm_data
[2023-06-28 10:01:17,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:01:17,652] [INFO] Task started: CheckM
[2023-06-28 10:01:17,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017642845.1_ASM1764284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017642845.1_ASM1764284v1_genomic.fna/checkm_input GCA_017642845.1_ASM1764284v1_genomic.fna/checkm_result
[2023-06-28 10:01:50,530] [INFO] Task succeeded: CheckM
[2023-06-28 10:01:50,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:01:50,555] [INFO] ===== Completeness check finished =====
[2023-06-28 10:01:50,556] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:01:50,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017642845.1_ASM1764284v1_genomic.fna/markers.fasta)
[2023-06-28 10:01:50,556] [INFO] Task started: Blastn
[2023-06-28 10:01:50,557] [INFO] Running command: blastn -query GCA_017642845.1_ASM1764284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9daff234-e7a9-466e-b5bb-a568943d5347/dqc_reference/reference_markers_gtdb.fasta -out GCA_017642845.1_ASM1764284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:52,345] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:52,351] [INFO] Selected 11 target genomes.
[2023-06-28 10:01:52,351] [INFO] Target genome list was writen to GCA_017642845.1_ASM1764284v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:01:52,354] [INFO] Task started: fastANI
[2023-06-28 10:01:52,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f71c2e2-7939-4e56-8465-448093f99d8b/GCA_017642845.1_ASM1764284v1_genomic.fna.gz --refList GCA_017642845.1_ASM1764284v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017642845.1_ASM1764284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:02:00,263] [INFO] Task succeeded: fastANI
[2023-06-28 10:02:00,278] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:02:00,278] [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_002480495.1	s__Parvibaculum sp002480495	99.1206	1058	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	conclusive
GCA_002842875.1	s__Parvibaculum sp002842875	84.1605	733	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359855.1	s__Parvibaculum sp014359855	83.6285	502	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694985.1	s__Parvibaculum sp002694985	83.6146	782	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017642695.1	s__Parvibaculum sp017642695	83.2025	828	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	82.4209	764	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823365.1	s__Parvibaculum sp013823365	81.6825	560	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000168975.1	s__Roseibium aggregatum	76.3535	95	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930675.1	s__CAIYZJ01 sp903930675	76.1408	57	1137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01	95.0	97.85	97.85	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-28 10:02:00,280] [INFO] GTDB search result was written to GCA_017642845.1_ASM1764284v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:02:00,281] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:02:00,286] [INFO] DFAST_QC result json was written to GCA_017642845.1_ASM1764284v1_genomic.fna/dqc_result.json
[2023-06-28 10:02:00,286] [INFO] DFAST_QC completed!
[2023-06-28 10:02:00,286] [INFO] Total running time: 0h1m10s