[2024-01-24 15:32:06,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:06,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:06,018] [INFO] DQC Reference Directory: /var/lib/cwl/stge22b7a0f-6041-46c9-8bf7-d637a03900c8/dqc_reference
[2024-01-24 15:32:07,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:07,214] [INFO] Task started: Prodigal
[2024-01-24 15:32:07,214] [INFO] Running command: gunzip -c /var/lib/cwl/stgf77aca3c-b9dd-4a84-98ab-78c42369831f/GCF_003367175.1_ASM336717v1_genomic.fna.gz | prodigal -d GCF_003367175.1_ASM336717v1_genomic.fna/cds.fna -a GCF_003367175.1_ASM336717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:30,114] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:30,115] [INFO] Task started: HMMsearch
[2024-01-24 15:32:30,115] [INFO] Running command: hmmsearch --tblout GCF_003367175.1_ASM336717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge22b7a0f-6041-46c9-8bf7-d637a03900c8/dqc_reference/reference_markers.hmm GCF_003367175.1_ASM336717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:30,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:30,470] [INFO] Found 6/6 markers.
[2024-01-24 15:32:30,645] [INFO] Query marker FASTA was written to GCF_003367175.1_ASM336717v1_genomic.fna/markers.fasta
[2024-01-24 15:32:30,646] [INFO] Task started: Blastn
[2024-01-24 15:32:30,646] [INFO] Running command: blastn -query GCF_003367175.1_ASM336717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge22b7a0f-6041-46c9-8bf7-d637a03900c8/dqc_reference/reference_markers.fasta -out GCF_003367175.1_ASM336717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:31,510] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:31,515] [INFO] Selected 13 target genomes.
[2024-01-24 15:32:31,515] [INFO] Target genome list was writen to GCF_003367175.1_ASM336717v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:31,552] [INFO] Task started: fastANI
[2024-01-24 15:32:31,553] [INFO] Running command: fastANI --query /var/lib/cwl/stgf77aca3c-b9dd-4a84-98ab-78c42369831f/GCF_003367175.1_ASM336717v1_genomic.fna.gz --refList GCF_003367175.1_ASM336717v1_genomic.fna/target_genomes.txt --output GCF_003367175.1_ASM336717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:51,778] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:51,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge22b7a0f-6041-46c9-8bf7-d637a03900c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:51,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge22b7a0f-6041-46c9-8bf7-d637a03900c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:51,790] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:32:51,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:51,791] [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
Trinickia dinghuensis	strain=DHOM06	GCA_003367175.1	2291023	2291023	type	True	100.0	2433	2433	95	conclusive
Trinickia dabaoshanensis	strain=GIMN1.004	GCA_002879885.1	564714	564714	type	True	83.9119	1342	2433	95	below_threshold
Trinickia diaoshuihuensis	strain=NEAU-SY24	GCA_003390925.1	2292265	2292265	type	True	83.506	1263	2433	95	below_threshold
Trinickia soli	strain=GP25-8	GCA_002879855.1	380675	380675	type	True	82.8046	1213	2433	95	below_threshold
Trinickia soli	strain=LMG 24076	GCA_902859815.1	380675	380675	type	True	82.7754	1217	2433	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	80.7415	967	2433	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	80.7094	937	2433	95	below_threshold
Trinickia symbiotica	strain=JPY-345	GCA_002934455.1	863227	863227	type	True	80.6708	978	2433	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	80.571	963	2433	95	below_threshold
Paraburkholderia phosphatilytica	strain=7QSK02	GCA_003443895.1	2282883	2282883	type	True	80.4724	1081	2433	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	80.3854	942	2433	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	80.2224	957	2433	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	80.1079	889	2433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:51,792] [INFO] DFAST Taxonomy check result was written to GCF_003367175.1_ASM336717v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:51,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:51,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:51,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge22b7a0f-6041-46c9-8bf7-d637a03900c8/dqc_reference/checkm_data
[2024-01-24 15:32:51,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:51,864] [INFO] Task started: CheckM
[2024-01-24 15:32:51,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367175.1_ASM336717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367175.1_ASM336717v1_genomic.fna/checkm_input GCF_003367175.1_ASM336717v1_genomic.fna/checkm_result
[2024-01-24 15:33:55,924] [INFO] Task succeeded: CheckM
[2024-01-24 15:33:55,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:33:55,947] [INFO] ===== Completeness check finished =====
[2024-01-24 15:33:55,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:33:55,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367175.1_ASM336717v1_genomic.fna/markers.fasta)
[2024-01-24 15:33:55,948] [INFO] Task started: Blastn
[2024-01-24 15:33:55,948] [INFO] Running command: blastn -query GCF_003367175.1_ASM336717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge22b7a0f-6041-46c9-8bf7-d637a03900c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367175.1_ASM336717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:33:57,383] [INFO] Task succeeded: Blastn
[2024-01-24 15:33:57,388] [INFO] Selected 9 target genomes.
[2024-01-24 15:33:57,388] [INFO] Target genome list was writen to GCF_003367175.1_ASM336717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:33:57,408] [INFO] Task started: fastANI
[2024-01-24 15:33:57,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgf77aca3c-b9dd-4a84-98ab-78c42369831f/GCF_003367175.1_ASM336717v1_genomic.fna.gz --refList GCF_003367175.1_ASM336717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367175.1_ASM336717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:34:11,436] [INFO] Task succeeded: fastANI
[2024-01-24 15:34:11,446] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:34:11,446] [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_003367175.1	s__Trinickia dinghuensis	100.0	2433	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017315725.1	s__Trinickia sp017315725	84.9716	1451	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879885.1	s__Trinickia dabaoshanensis	83.9028	1344	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390925.1	s__Trinickia diaoshuihuensis	83.5054	1263	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879855.1	s__Trinickia soli	82.7882	1216	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	99.68	99.37	0.95	0.90	3	-
GCA_004322045.1	s__Trinickia sp004322045	82.6373	1173	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	96.62	96.62	0.93	0.93	2	-
GCF_003628145.1	s__Trinickia fusca	81.9895	979	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499075.1	s__Burkholderia pseudomultivorans	80.6844	942	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.22	95.54	0.83	0.81	13	-
GCF_003443895.1	s__Paraburkholderia phosphatilytica	80.4923	1078	2433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:34:11,448] [INFO] GTDB search result was written to GCF_003367175.1_ASM336717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:34:11,449] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:34:11,453] [INFO] DFAST_QC result json was written to GCF_003367175.1_ASM336717v1_genomic.fna/dqc_result.json
[2024-01-24 15:34:11,453] [INFO] DFAST_QC completed!
[2024-01-24 15:34:11,453] [INFO] Total running time: 0h2m5s