[2024-01-24 10:57:19,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:19,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:19,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg38f42505-7108-4cc3-9471-e5638aa9feb3/dqc_reference
[2024-01-24 10:57:22,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,298] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,298] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b220c93-f82f-491d-99af-69abf50205ec/GCF_001591385.1_ASM159138v1_genomic.fna.gz | prodigal -d GCF_001591385.1_ASM159138v1_genomic.fna/cds.fna -a GCF_001591385.1_ASM159138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:39,971] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:39,972] [INFO] Task started: HMMsearch
[2024-01-24 10:57:39,972] [INFO] Running command: hmmsearch --tblout GCF_001591385.1_ASM159138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38f42505-7108-4cc3-9471-e5638aa9feb3/dqc_reference/reference_markers.hmm GCF_001591385.1_ASM159138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:40,307] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:40,309] [INFO] Found 6/6 markers.
[2024-01-24 10:57:40,363] [INFO] Query marker FASTA was written to GCF_001591385.1_ASM159138v1_genomic.fna/markers.fasta
[2024-01-24 10:57:40,364] [INFO] Task started: Blastn
[2024-01-24 10:57:40,364] [INFO] Running command: blastn -query GCF_001591385.1_ASM159138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38f42505-7108-4cc3-9471-e5638aa9feb3/dqc_reference/reference_markers.fasta -out GCF_001591385.1_ASM159138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:41,416] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:41,421] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:41,422] [INFO] Target genome list was writen to GCF_001591385.1_ASM159138v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:41,466] [INFO] Task started: fastANI
[2024-01-24 10:57:41,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b220c93-f82f-491d-99af-69abf50205ec/GCF_001591385.1_ASM159138v1_genomic.fna.gz --refList GCF_001591385.1_ASM159138v1_genomic.fna/target_genomes.txt --output GCF_001591385.1_ASM159138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,210] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38f42505-7108-4cc3-9471-e5638aa9feb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38f42505-7108-4cc3-9471-e5638aa9feb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,227] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:01,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:01,227] [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 soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	100.0	1736	1744	95	conclusive
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	83.8886	1078	1744	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	83.7835	1102	1744	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	83.6797	1109	1744	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	83.5064	1104	1744	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	83.1545	932	1744	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.4244	696	1744	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.3582	754	1744	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	81.0698	613	1744	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.0399	698	1744	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.9452	802	1744	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.8913	716	1744	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.1204	679	1744	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	80.0919	571	1744	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	80.0601	573	1744	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	78.9949	629	1744	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	78.7027	576	1744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,229] [INFO] DFAST Taxonomy check result was written to GCF_001591385.1_ASM159138v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38f42505-7108-4cc3-9471-e5638aa9feb3/dqc_reference/checkm_data
[2024-01-24 10:58:01,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:01,289] [INFO] Task started: CheckM
[2024-01-24 10:58:01,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591385.1_ASM159138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591385.1_ASM159138v1_genomic.fna/checkm_input GCF_001591385.1_ASM159138v1_genomic.fna/checkm_result
[2024-01-24 10:59:14,571] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:14,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:14,597] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:14,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:14,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591385.1_ASM159138v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:14,598] [INFO] Task started: Blastn
[2024-01-24 10:59:14,598] [INFO] Running command: blastn -query GCF_001591385.1_ASM159138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38f42505-7108-4cc3-9471-e5638aa9feb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591385.1_ASM159138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:16,813] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:16,817] [INFO] Selected 7 target genomes.
[2024-01-24 10:59:16,817] [INFO] Target genome list was writen to GCF_001591385.1_ASM159138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:16,824] [INFO] Task started: fastANI
[2024-01-24 10:59:16,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b220c93-f82f-491d-99af-69abf50205ec/GCF_001591385.1_ASM159138v1_genomic.fna.gz --refList GCF_001591385.1_ASM159138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591385.1_ASM159138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:27,648] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:27,659] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:27,659] [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_001591385.1	s__Variovorax soli	100.0	1736	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018241225.1	s__Variovorax sp018241225	89.9836	1364	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241905.1	s__Variovorax sp018241905	89.8445	971	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217005.1	s__Variovorax sp004217005	87.8384	1303	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.70	99.70	0.95	0.95	2	-
GCF_900114785.1	s__Variovorax sp900114785	87.7331	1313	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340105.1	s__Variovorax sp004340105	86.4698	1258	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016082275.1	s__Variovorax sp016082275	83.6992	1045	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:27,662] [INFO] GTDB search result was written to GCF_001591385.1_ASM159138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:27,663] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:27,666] [INFO] DFAST_QC result json was written to GCF_001591385.1_ASM159138v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:27,667] [INFO] DFAST_QC completed!
[2024-01-24 10:59:27,667] [INFO] Total running time: 0h2m8s