[2024-01-24 14:23:02,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:02,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:02,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e4ba3ba-7438-44e4-b75c-18d62ea338f1/dqc_reference
[2024-01-24 14:23:03,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:03,650] [INFO] Task started: Prodigal
[2024-01-24 14:23:03,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg63e895a2-5298-4a1f-b4e1-0929e7886c49/GCF_014284305.1_ASM1428430v1_genomic.fna.gz | prodigal -d GCF_014284305.1_ASM1428430v1_genomic.fna/cds.fna -a GCF_014284305.1_ASM1428430v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:18,388] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:18,388] [INFO] Task started: HMMsearch
[2024-01-24 14:23:18,388] [INFO] Running command: hmmsearch --tblout GCF_014284305.1_ASM1428430v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e4ba3ba-7438-44e4-b75c-18d62ea338f1/dqc_reference/reference_markers.hmm GCF_014284305.1_ASM1428430v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:18,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:18,808] [INFO] Found 6/6 markers.
[2024-01-24 14:23:18,876] [INFO] Query marker FASTA was written to GCF_014284305.1_ASM1428430v1_genomic.fna/markers.fasta
[2024-01-24 14:23:18,876] [INFO] Task started: Blastn
[2024-01-24 14:23:18,877] [INFO] Running command: blastn -query GCF_014284305.1_ASM1428430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4ba3ba-7438-44e4-b75c-18d62ea338f1/dqc_reference/reference_markers.fasta -out GCF_014284305.1_ASM1428430v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:20,784] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:20,788] [INFO] Selected 16 target genomes.
[2024-01-24 14:23:20,788] [INFO] Target genome list was writen to GCF_014284305.1_ASM1428430v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:20,833] [INFO] Task started: fastANI
[2024-01-24 14:23:20,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e895a2-5298-4a1f-b4e1-0929e7886c49/GCF_014284305.1_ASM1428430v1_genomic.fna.gz --refList GCF_014284305.1_ASM1428430v1_genomic.fna/target_genomes.txt --output GCF_014284305.1_ASM1428430v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:36,384] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:36,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e4ba3ba-7438-44e4-b75c-18d62ea338f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:36,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e4ba3ba-7438-44e4-b75c-18d62ea338f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:36,438] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:36,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:36,438] [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
Undibacterium seohonense	strain=KACC 16656	GCA_014284305.1	1344950	1344950	type	True	100.0	1574	1578	95	conclusive
Undibacterium amnicola	strain=KCTC 52442	GCA_014284275.1	1834038	1834038	type	True	83.6054	842	1578	95	below_threshold
Undibacterium flavidum	strain=LX15W	GCA_014284175.1	2762297	2762297	type	True	81.8234	687	1578	95	below_threshold
Undibacterium baiyunense	strain=BYS107W	GCA_018139645.1	2828731	2828731	type	True	81.1315	721	1578	95	below_threshold
Undibacterium macrobrachii	strain=KCTC 23916	GCA_014652415.1	1119058	1119058	type	True	81.0824	689	1578	95	below_threshold
Undibacterium fentianense	strain=FT137W	GCA_018139545.1	2828728	2828728	type	True	80.8392	498	1578	95	below_threshold
Undibacterium nitidum	strain=LX22W	GCA_014284155.1	2762298	2762298	type	True	79.9464	377	1578	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	78.4203	197	1578	95	below_threshold
Undibacterium parvum	strain=DSM 23061	GCA_003955735.1	401471	401471	type	True	78.3176	214	1578	95	below_threshold
Undibacterium aquatile	strain=CCTCC AB 2015119	GCA_014699135.1	1537398	1537398	type	True	78.2464	203	1578	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:36,440] [INFO] DFAST Taxonomy check result was written to GCF_014284305.1_ASM1428430v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:36,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:36,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:36,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e4ba3ba-7438-44e4-b75c-18d62ea338f1/dqc_reference/checkm_data
[2024-01-24 14:23:36,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:36,509] [INFO] Task started: CheckM
[2024-01-24 14:23:36,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284305.1_ASM1428430v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284305.1_ASM1428430v1_genomic.fna/checkm_input GCF_014284305.1_ASM1428430v1_genomic.fna/checkm_result
[2024-01-24 14:24:26,259] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:26,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:26,282] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:26,282] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:26,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284305.1_ASM1428430v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:26,283] [INFO] Task started: Blastn
[2024-01-24 14:24:26,283] [INFO] Running command: blastn -query GCF_014284305.1_ASM1428430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4ba3ba-7438-44e4-b75c-18d62ea338f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284305.1_ASM1428430v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:27,837] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:27,841] [INFO] Selected 11 target genomes.
[2024-01-24 14:24:27,842] [INFO] Target genome list was writen to GCF_014284305.1_ASM1428430v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:27,862] [INFO] Task started: fastANI
[2024-01-24 14:24:27,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e895a2-5298-4a1f-b4e1-0929e7886c49/GCF_014284305.1_ASM1428430v1_genomic.fna.gz --refList GCF_014284305.1_ASM1428430v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284305.1_ASM1428430v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:38,356] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:38,425] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:38,426] [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_014284305.1	s__Undibacterium seohonense	100.0	1574	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002482715.1	s__Undibacterium sp002482715	84.2389	634	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284275.1	s__Undibacterium amnicola	83.6212	841	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284175.1	s__Undibacterium sp014284175	81.8082	687	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139645.1	s__Undibacterium sp018139645	81.128	722	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652415.1	s__Undibacterium macrobrachii	81.0814	687	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139545.1	s__Undibacterium sp018139545	80.8514	497	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284115.1	s__Undibacterium sp014284115	79.9058	382	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016200845.1	s__Undibacterium sp016200845	78.8733	325	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284255.1	s__Undibacterium jejuense	78.3916	199	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699135.1	s__Undibacterium aquatile	78.2464	203	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	96.61	96.29	0.93	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:38,427] [INFO] GTDB search result was written to GCF_014284305.1_ASM1428430v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:38,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:38,432] [INFO] DFAST_QC result json was written to GCF_014284305.1_ASM1428430v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:38,432] [INFO] DFAST_QC completed!
[2024-01-24 14:24:38,432] [INFO] Total running time: 0h1m36s