[2024-01-24 12:34:20,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg638d1b4d-22e5-41da-8ef6-d26f66d012bf/dqc_reference
[2024-01-24 12:34:21,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,788] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg00779ad2-150e-4b21-8bc1-446aad192ac8/GCF_003415675.1_ASM341567v1_genomic.fna.gz | prodigal -d GCF_003415675.1_ASM341567v1_genomic.fna/cds.fna -a GCF_003415675.1_ASM341567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:39,929] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:39,929] [INFO] Task started: HMMsearch
[2024-01-24 12:34:39,930] [INFO] Running command: hmmsearch --tblout GCF_003415675.1_ASM341567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg638d1b4d-22e5-41da-8ef6-d26f66d012bf/dqc_reference/reference_markers.hmm GCF_003415675.1_ASM341567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:40,231] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:40,233] [INFO] Found 6/6 markers.
[2024-01-24 12:34:40,272] [INFO] Query marker FASTA was written to GCF_003415675.1_ASM341567v1_genomic.fna/markers.fasta
[2024-01-24 12:34:40,272] [INFO] Task started: Blastn
[2024-01-24 12:34:40,272] [INFO] Running command: blastn -query GCF_003415675.1_ASM341567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg638d1b4d-22e5-41da-8ef6-d26f66d012bf/dqc_reference/reference_markers.fasta -out GCF_003415675.1_ASM341567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:41,187] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:41,192] [INFO] Selected 24 target genomes.
[2024-01-24 12:34:41,192] [INFO] Target genome list was writen to GCF_003415675.1_ASM341567v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:41,202] [INFO] Task started: fastANI
[2024-01-24 12:34:41,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg00779ad2-150e-4b21-8bc1-446aad192ac8/GCF_003415675.1_ASM341567v1_genomic.fna.gz --refList GCF_003415675.1_ASM341567v1_genomic.fna/target_genomes.txt --output GCF_003415675.1_ASM341567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:35:01,708] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:01,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg638d1b4d-22e5-41da-8ef6-d26f66d012bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:35:01,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg638d1b4d-22e5-41da-8ef6-d26f66d012bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:35:01,728] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:35:01,728] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:35:01,728] [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
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	100.0	1597	1601	95	conclusive
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	80.5718	620	1601	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	80.4099	643	1601	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	80.3855	593	1601	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	79.7121	531	1601	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	79.5212	416	1601	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	79.521	490	1601	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	79.5169	539	1601	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.4291	548	1601	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.3925	501	1601	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	79.1574	449	1601	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	78.9852	540	1601	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	78.9068	534	1601	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	78.8883	532	1601	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	78.8839	551	1601	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	78.8783	521	1601	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	78.8315	492	1601	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.8083	454	1601	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.8038	388	1601	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	78.753	388	1601	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	78.7505	318	1601	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	78.5294	401	1601	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.5241	393	1601	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	77.4021	261	1601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:35:01,730] [INFO] DFAST Taxonomy check result was written to GCF_003415675.1_ASM341567v1_genomic.fna/tc_result.tsv
[2024-01-24 12:35:01,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:35:01,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:35:01,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg638d1b4d-22e5-41da-8ef6-d26f66d012bf/dqc_reference/checkm_data
[2024-01-24 12:35:01,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:35:01,782] [INFO] Task started: CheckM
[2024-01-24 12:35:01,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003415675.1_ASM341567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003415675.1_ASM341567v1_genomic.fna/checkm_input GCF_003415675.1_ASM341567v1_genomic.fna/checkm_result
[2024-01-24 12:35:59,431] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:59,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:59,453] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:59,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:59,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003415675.1_ASM341567v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:59,454] [INFO] Task started: Blastn
[2024-01-24 12:35:59,455] [INFO] Running command: blastn -query GCF_003415675.1_ASM341567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg638d1b4d-22e5-41da-8ef6-d26f66d012bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_003415675.1_ASM341567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:01,061] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:01,065] [INFO] Selected 17 target genomes.
[2024-01-24 12:36:01,066] [INFO] Target genome list was writen to GCF_003415675.1_ASM341567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:36:01,095] [INFO] Task started: fastANI
[2024-01-24 12:36:01,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg00779ad2-150e-4b21-8bc1-446aad192ac8/GCF_003415675.1_ASM341567v1_genomic.fna.gz --refList GCF_003415675.1_ASM341567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003415675.1_ASM341567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:36:18,556] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:18,573] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:36:18,573] [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_003415675.1	s__Rhodoferax sp003415675	100.0	1597	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903886275.1	s__Rhodoferax sp903886275	83.758	924	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.88	99.42	0.96	0.95	10	-
GCA_903845935.1	s__Rhodoferax sp903845935	83.1997	771	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.58	99.41	0.92	0.88	22	-
GCA_903876045.1	s__Rhodoferax sp903876045	81.1838	654	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.28	99.14	0.84	0.81	3	-
GCF_002943465.1	s__Rhodoferax sp002943465	80.985	648	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870955.1	s__Rhodoferax sp903870955	80.9097	545	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.51	98.51	0.73	0.73	2	-
GCA_001795455.1	s__Rhodoferax sp001795455	80.8917	644	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCF_001955715.1	s__Rhodoferax saidenbachensis	80.449	638	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903863395.1	s__Rhodoferax sp903863395	80.2333	437	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.94	98.87	0.83	0.81	5	-
GCF_900104385.1	s__Rhodoferax_B sp900104385	79.4722	580	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391545.1	s__Rhodoferax sp011391545	79.2934	364	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853895.1	s__Rhodoferax sp903853895	79.2011	496	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.86	99.86	0.86	0.86	2	-
GCF_001428625.1	s__Hydrogenophaga sp001428625	79.1954	504	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703145.1	s__Ottowia sp016703145	79.0061	436	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.21	99.21	0.89	0.89	2	-
GCA_002083775.1	s__Rhodoferax ferrireducens_A	78.8329	518	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	77.9065	457	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	77.8207	461	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:36:18,575] [INFO] GTDB search result was written to GCF_003415675.1_ASM341567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:36:18,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:36:18,579] [INFO] DFAST_QC result json was written to GCF_003415675.1_ASM341567v1_genomic.fna/dqc_result.json
[2024-01-24 12:36:18,580] [INFO] DFAST_QC completed!
[2024-01-24 12:36:18,580] [INFO] Total running time: 0h1m58s