[2024-01-24 13:28:12,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:12,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:12,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg36a88553-17e9-4d94-b6a2-bf0f9a4741bd/dqc_reference
[2024-01-24 13:28:14,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,106] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,106] [INFO] Running command: gunzip -c /var/lib/cwl/stga02df63c-419b-4419-98f6-7c0086efa2d5/GCF_000688255.1_ASM68825v1_genomic.fna.gz | prodigal -d GCF_000688255.1_ASM68825v1_genomic.fna/cds.fna -a GCF_000688255.1_ASM68825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:27,697] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:27,697] [INFO] Task started: HMMsearch
[2024-01-24 13:28:27,697] [INFO] Running command: hmmsearch --tblout GCF_000688255.1_ASM68825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36a88553-17e9-4d94-b6a2-bf0f9a4741bd/dqc_reference/reference_markers.hmm GCF_000688255.1_ASM68825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:28,148] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:28,149] [INFO] Found 6/6 markers.
[2024-01-24 13:28:28,182] [INFO] Query marker FASTA was written to GCF_000688255.1_ASM68825v1_genomic.fna/markers.fasta
[2024-01-24 13:28:28,182] [INFO] Task started: Blastn
[2024-01-24 13:28:28,182] [INFO] Running command: blastn -query GCF_000688255.1_ASM68825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36a88553-17e9-4d94-b6a2-bf0f9a4741bd/dqc_reference/reference_markers.fasta -out GCF_000688255.1_ASM68825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:29,147] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:29,150] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:29,150] [INFO] Target genome list was writen to GCF_000688255.1_ASM68825v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:29,172] [INFO] Task started: fastANI
[2024-01-24 13:28:29,172] [INFO] Running command: fastANI --query /var/lib/cwl/stga02df63c-419b-4419-98f6-7c0086efa2d5/GCF_000688255.1_ASM68825v1_genomic.fna.gz --refList GCF_000688255.1_ASM68825v1_genomic.fna/target_genomes.txt --output GCF_000688255.1_ASM68825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:45,706] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:45,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36a88553-17e9-4d94-b6a2-bf0f9a4741bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:45,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36a88553-17e9-4d94-b6a2-bf0f9a4741bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:45,720] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:45,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:45,721] [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
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	100.0	1182	1182	95	conclusive
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	81.3325	666	1182	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	81.2861	677	1182	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.1207	563	1182	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	79.895	600	1182	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	79.7107	532	1182	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	79.7068	552	1182	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.5361	516	1182	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	79.4936	567	1182	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.4578	536	1182	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	79.3598	568	1182	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	79.3318	523	1182	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	78.6637	462	1182	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	78.4771	413	1182	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	78.2113	358	1182	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.0793	341	1182	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.0553	358	1182	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.7833	373	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:45,722] [INFO] DFAST Taxonomy check result was written to GCF_000688255.1_ASM68825v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:45,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:45,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:45,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36a88553-17e9-4d94-b6a2-bf0f9a4741bd/dqc_reference/checkm_data
[2024-01-24 13:28:45,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:45,766] [INFO] Task started: CheckM
[2024-01-24 13:28:45,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000688255.1_ASM68825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000688255.1_ASM68825v1_genomic.fna/checkm_input GCF_000688255.1_ASM68825v1_genomic.fna/checkm_result
[2024-01-24 13:29:27,521] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:27,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:27,545] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:27,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:27,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000688255.1_ASM68825v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:27,546] [INFO] Task started: Blastn
[2024-01-24 13:29:27,546] [INFO] Running command: blastn -query GCF_000688255.1_ASM68825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36a88553-17e9-4d94-b6a2-bf0f9a4741bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000688255.1_ASM68825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:29,321] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:29,324] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:29,324] [INFO] Target genome list was writen to GCF_000688255.1_ASM68825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:29,349] [INFO] Task started: fastANI
[2024-01-24 13:29:29,350] [INFO] Running command: fastANI --query /var/lib/cwl/stga02df63c-419b-4419-98f6-7c0086efa2d5/GCF_000688255.1_ASM68825v1_genomic.fna.gz --refList GCF_000688255.1_ASM68825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000688255.1_ASM68825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:38,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:38,816] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:38,816] [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_000688255.1	s__Giesbergeria psychrophila	100.0	1182	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017988165.1	s__Giesbergeria sp017988165	84.3664	507	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017987055.1	s__Giesbergeria sp017987055	83.6325	413	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.05	99.05	0.76	0.76	2	-
GCA_903882725.1	s__Giesbergeria sp903882725	83.0246	345	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	81.4172	675	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_004341365.1	s__Giesbergeria metamorpha	81.2879	677	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
GCF_002176815.1	s__Acidovorax sp002176815	80.3041	600	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.23	97.20	0.91	0.82	4	-
GCF_003096555.1	s__Giesbergeria sp003096555	79.9672	594	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCA_017985015.1	s__Giesbergeria sp017985015	79.8295	488	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.01	95.86	0.92	0.90	6	-
GCA_001770955.1	s__Giesbergeria sp001770955	79.7668	561	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_001633105.1	s__Acidovorax sp001633105	79.7396	578	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739995.1	s__Giesbergeria granuli	79.3742	548	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_900111115.1	s__Giesbergeria anulus	78.8404	380	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:38,818] [INFO] GTDB search result was written to GCF_000688255.1_ASM68825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:38,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:38,821] [INFO] DFAST_QC result json was written to GCF_000688255.1_ASM68825v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:38,822] [INFO] DFAST_QC completed!
[2024-01-24 13:29:38,822] [INFO] Total running time: 0h1m26s