[2023-06-19 07:29:19,839] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:29:19,842] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:29:19,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f3c421c-4a28-4b55-87f8-1cd68786a8c9/dqc_reference
[2023-06-19 07:29:22,498] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:29:22,499] [INFO] Task started: Prodigal
[2023-06-19 07:29:22,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c1e6d4d-47c2-4a5f-85c0-aebf0f97fe7d/GCA_018241185.1_ASM1824118v1_genomic.fna.gz | prodigal -d GCA_018241185.1_ASM1824118v1_genomic.fna/cds.fna -a GCA_018241185.1_ASM1824118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:29:38,093] [INFO] Task succeeded: Prodigal
[2023-06-19 07:29:38,093] [INFO] Task started: HMMsearch
[2023-06-19 07:29:38,093] [INFO] Running command: hmmsearch --tblout GCA_018241185.1_ASM1824118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f3c421c-4a28-4b55-87f8-1cd68786a8c9/dqc_reference/reference_markers.hmm GCA_018241185.1_ASM1824118v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:29:38,336] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:29:38,337] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6c1e6d4d-47c2-4a5f-85c0-aebf0f97fe7d/GCA_018241185.1_ASM1824118v1_genomic.fna.gz]
[2023-06-19 07:29:38,380] [INFO] Query marker FASTA was written to GCA_018241185.1_ASM1824118v1_genomic.fna/markers.fasta
[2023-06-19 07:29:38,381] [INFO] Task started: Blastn
[2023-06-19 07:29:38,381] [INFO] Running command: blastn -query GCA_018241185.1_ASM1824118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f3c421c-4a28-4b55-87f8-1cd68786a8c9/dqc_reference/reference_markers.fasta -out GCA_018241185.1_ASM1824118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:29:39,355] [INFO] Task succeeded: Blastn
[2023-06-19 07:29:39,359] [INFO] Selected 16 target genomes.
[2023-06-19 07:29:39,359] [INFO] Target genome list was writen to GCA_018241185.1_ASM1824118v1_genomic.fna/target_genomes.txt
[2023-06-19 07:29:39,360] [INFO] Task started: fastANI
[2023-06-19 07:29:39,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c1e6d4d-47c2-4a5f-85c0-aebf0f97fe7d/GCA_018241185.1_ASM1824118v1_genomic.fna.gz --refList GCA_018241185.1_ASM1824118v1_genomic.fna/target_genomes.txt --output GCA_018241185.1_ASM1824118v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:29:56,939] [INFO] Task succeeded: fastANI
[2023-06-19 07:29:56,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f3c421c-4a28-4b55-87f8-1cd68786a8c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:29:56,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f3c421c-4a28-4b55-87f8-1cd68786a8c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:29:56,953] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:29:56,953] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 07:29:56,954] [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
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	83.4375	1026	1641	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	83.239	1099	1641	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	83.22	1034	1641	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	83.0496	1032	1641	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	82.9413	900	1641	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	82.6937	930	1641	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.2616	711	1641	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.0675	648	1641	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.9065	710	1641	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.6765	699	1641	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.6043	637	1641	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.4037	651	1641	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	79.8959	678	1641	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	79.2159	568	1641	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	79.1671	522	1641	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	78.6308	515	1641	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 07:29:56,956] [INFO] DFAST Taxonomy check result was written to GCA_018241185.1_ASM1824118v1_genomic.fna/tc_result.tsv
[2023-06-19 07:29:56,956] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:29:56,956] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:29:56,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f3c421c-4a28-4b55-87f8-1cd68786a8c9/dqc_reference/checkm_data
[2023-06-19 07:29:56,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:29:57,005] [INFO] Task started: CheckM
[2023-06-19 07:29:57,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018241185.1_ASM1824118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018241185.1_ASM1824118v1_genomic.fna/checkm_input GCA_018241185.1_ASM1824118v1_genomic.fna/checkm_result
[2023-06-19 07:31:01,416] [INFO] Task succeeded: CheckM
[2023-06-19 07:31:01,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 07:31:01,432] [INFO] ===== Completeness check finished =====
[2023-06-19 07:31:01,432] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:31:01,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018241185.1_ASM1824118v1_genomic.fna/markers.fasta)
[2023-06-19 07:31:01,433] [INFO] Task started: Blastn
[2023-06-19 07:31:01,433] [INFO] Running command: blastn -query GCA_018241185.1_ASM1824118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f3c421c-4a28-4b55-87f8-1cd68786a8c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018241185.1_ASM1824118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:31:03,373] [INFO] Task succeeded: Blastn
[2023-06-19 07:31:03,376] [INFO] Selected 9 target genomes.
[2023-06-19 07:31:03,376] [INFO] Target genome list was writen to GCA_018241185.1_ASM1824118v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:31:03,382] [INFO] Task started: fastANI
[2023-06-19 07:31:03,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c1e6d4d-47c2-4a5f-85c0-aebf0f97fe7d/GCA_018241185.1_ASM1824118v1_genomic.fna.gz --refList GCA_018241185.1_ASM1824118v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018241185.1_ASM1824118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:31:17,150] [INFO] Task succeeded: fastANI
[2023-06-19 07:31:17,159] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:31:17,159] [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_018241185.1	s__ALPHA2B sp018241185	100.0	1629	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_901875635.1	s__ALPHA2B sp901875635	92.7793	1292	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	99.68	99.68	0.89	0.89	2	-
GCF_003671765.1	s__ALPHA2B sp003671765	92.1532	1342	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503065.1	s__ALPHA2B sp005503065	91.3771	1283	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745855.1	s__Xenophilus azovorans	85.2339	1092	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806145.1	s__Variovorax sp900115375	83.4766	1140	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	96.08	95.68	0.83	0.79	13	-
GCF_014170375.1	s__Variovorax sp014170375	83.4646	1018	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376045.1	s__Variovorax sp013376045	83.3414	1081	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090195.1	s__Variovorax sp900090195	81.8877	932	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 07:31:17,161] [INFO] GTDB search result was written to GCA_018241185.1_ASM1824118v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:31:17,162] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:31:17,167] [INFO] DFAST_QC result json was written to GCA_018241185.1_ASM1824118v1_genomic.fna/dqc_result.json
[2023-06-19 07:31:17,167] [INFO] DFAST_QC completed!
[2023-06-19 07:31:17,167] [INFO] Total running time: 0h1m57s