[2024-01-24 13:27:46,579] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,581] [INFO] DQC Reference Directory: /var/lib/cwl/stge338421d-d8bc-444f-8810-30addc599b7f/dqc_reference
[2024-01-24 13:27:47,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,928] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,929] [INFO] Running command: gunzip -c /var/lib/cwl/stgae911a0c-8a08-473c-b186-aad224c6d73a/GCF_014284175.1_ASM1428417v1_genomic.fna.gz | prodigal -d GCF_014284175.1_ASM1428417v1_genomic.fna/cds.fna -a GCF_014284175.1_ASM1428417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:05,943] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:05,944] [INFO] Task started: HMMsearch
[2024-01-24 13:28:05,944] [INFO] Running command: hmmsearch --tblout GCF_014284175.1_ASM1428417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge338421d-d8bc-444f-8810-30addc599b7f/dqc_reference/reference_markers.hmm GCF_014284175.1_ASM1428417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:06,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:06,341] [INFO] Found 6/6 markers.
[2024-01-24 13:28:06,383] [INFO] Query marker FASTA was written to GCF_014284175.1_ASM1428417v1_genomic.fna/markers.fasta
[2024-01-24 13:28:06,384] [INFO] Task started: Blastn
[2024-01-24 13:28:06,384] [INFO] Running command: blastn -query GCF_014284175.1_ASM1428417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge338421d-d8bc-444f-8810-30addc599b7f/dqc_reference/reference_markers.fasta -out GCF_014284175.1_ASM1428417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:07,056] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:07,059] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:07,059] [INFO] Target genome list was writen to GCF_014284175.1_ASM1428417v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:07,065] [INFO] Task started: fastANI
[2024-01-24 13:28:07,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgae911a0c-8a08-473c-b186-aad224c6d73a/GCF_014284175.1_ASM1428417v1_genomic.fna.gz --refList GCF_014284175.1_ASM1428417v1_genomic.fna/target_genomes.txt --output GCF_014284175.1_ASM1428417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:16,570] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:16,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge338421d-d8bc-444f-8810-30addc599b7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:16,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge338421d-d8bc-444f-8810-30addc599b7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:16,578] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:16,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:16,578] [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 flavidum	strain=LX15W	GCA_014284175.1	2762297	2762297	type	True	100.0	1694	1695	95	conclusive
Undibacterium amnicola	strain=KCTC 52442	GCA_014284275.1	1834038	1834038	type	True	83.6413	776	1695	95	below_threshold
Undibacterium seohonense	strain=KACC 16656	GCA_014284305.1	1344950	1344950	type	True	81.5924	712	1695	95	below_threshold
Undibacterium fentianense	strain=FT137W	GCA_018139545.1	2828728	2828728	type	True	80.8632	512	1695	95	below_threshold
Undibacterium macrobrachii	strain=KCTC 23916	GCA_014652415.1	1119058	1119058	type	True	80.5595	638	1695	95	below_threshold
Undibacterium baiyunense	strain=BYS107W	GCA_018139645.1	2828731	2828731	type	True	80.3741	647	1695	95	below_threshold
Undibacterium nitidum	strain=LX22W	GCA_014284155.1	2762298	2762298	type	True	79.9053	380	1695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:16,580] [INFO] DFAST Taxonomy check result was written to GCF_014284175.1_ASM1428417v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:16,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:16,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:16,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge338421d-d8bc-444f-8810-30addc599b7f/dqc_reference/checkm_data
[2024-01-24 13:28:16,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:16,632] [INFO] Task started: CheckM
[2024-01-24 13:28:16,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284175.1_ASM1428417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284175.1_ASM1428417v1_genomic.fna/checkm_input GCF_014284175.1_ASM1428417v1_genomic.fna/checkm_result
[2024-01-24 13:29:08,021] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:08,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:08,043] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:08,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:08,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284175.1_ASM1428417v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:08,044] [INFO] Task started: Blastn
[2024-01-24 13:29:08,044] [INFO] Running command: blastn -query GCF_014284175.1_ASM1428417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge338421d-d8bc-444f-8810-30addc599b7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284175.1_ASM1428417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:08,893] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:08,896] [INFO] Selected 8 target genomes.
[2024-01-24 13:29:08,896] [INFO] Target genome list was writen to GCF_014284175.1_ASM1428417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:08,905] [INFO] Task started: fastANI
[2024-01-24 13:29:08,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgae911a0c-8a08-473c-b186-aad224c6d73a/GCF_014284175.1_ASM1428417v1_genomic.fna.gz --refList GCF_014284175.1_ASM1428417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284175.1_ASM1428417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:16,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:16,743] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:16,744] [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_014284175.1	s__Undibacterium sp014284175	100.0	1694	1695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014284275.1	s__Undibacterium amnicola	83.6582	775	1695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482715.1	s__Undibacterium sp002482715	81.8255	562	1695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284305.1	s__Undibacterium seohonense	81.6103	710	1695	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	80.8758	511	1695	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	80.5571	639	1695	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	80.3834	646	1695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200845.1	s__Undibacterium sp016200845	79.423	314	1695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:16,746] [INFO] GTDB search result was written to GCF_014284175.1_ASM1428417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:16,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:16,751] [INFO] DFAST_QC result json was written to GCF_014284175.1_ASM1428417v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:16,751] [INFO] DFAST_QC completed!
[2024-01-24 13:29:16,751] [INFO] Total running time: 0h1m30s