[2023-06-13 18:13:07,802] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:13:07,804] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:13:07,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg4929c480-93eb-40bf-a519-f4015ffdd94f/dqc_reference
[2023-06-13 18:13:08,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:13:08,913] [INFO] Task started: Prodigal
[2023-06-13 18:13:08,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d451878-354c-44b4-9177-45773d60e344/GCA_947484455.1_TH-Jun18-202_genomic.fna.gz | prodigal -d GCA_947484455.1_TH-Jun18-202_genomic.fna/cds.fna -a GCA_947484455.1_TH-Jun18-202_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:13:13,257] [INFO] Task succeeded: Prodigal
[2023-06-13 18:13:13,257] [INFO] Task started: HMMsearch
[2023-06-13 18:13:13,257] [INFO] Running command: hmmsearch --tblout GCA_947484455.1_TH-Jun18-202_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4929c480-93eb-40bf-a519-f4015ffdd94f/dqc_reference/reference_markers.hmm GCA_947484455.1_TH-Jun18-202_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:13:13,427] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:13:13,428] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2d451878-354c-44b4-9177-45773d60e344/GCA_947484455.1_TH-Jun18-202_genomic.fna.gz]
[2023-06-13 18:13:13,449] [INFO] Query marker FASTA was written to GCA_947484455.1_TH-Jun18-202_genomic.fna/markers.fasta
[2023-06-13 18:13:13,449] [INFO] Task started: Blastn
[2023-06-13 18:13:13,449] [INFO] Running command: blastn -query GCA_947484455.1_TH-Jun18-202_genomic.fna/markers.fasta -db /var/lib/cwl/stg4929c480-93eb-40bf-a519-f4015ffdd94f/dqc_reference/reference_markers.fasta -out GCA_947484455.1_TH-Jun18-202_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:13:14,030] [INFO] Task succeeded: Blastn
[2023-06-13 18:13:14,033] [INFO] Selected 19 target genomes.
[2023-06-13 18:13:14,034] [INFO] Target genome list was writen to GCA_947484455.1_TH-Jun18-202_genomic.fna/target_genomes.txt
[2023-06-13 18:13:14,035] [INFO] Task started: fastANI
[2023-06-13 18:13:14,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d451878-354c-44b4-9177-45773d60e344/GCA_947484455.1_TH-Jun18-202_genomic.fna.gz --refList GCA_947484455.1_TH-Jun18-202_genomic.fna/target_genomes.txt --output GCA_947484455.1_TH-Jun18-202_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:13:29,810] [INFO] Task succeeded: fastANI
[2023-06-13 18:13:29,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4929c480-93eb-40bf-a519-f4015ffdd94f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:13:29,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4929c480-93eb-40bf-a519-f4015ffdd94f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:13:29,819] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:13:29,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:13:29,819] [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
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.6824	58	551	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	76.5907	51	551	95	below_threshold
Bradyrhizobium campsiandrae	strain=INPA 394B	GCA_014529705.1	1729892	1729892	type	True	76.4225	66	551	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	76.262	60	551	95	below_threshold
Bradyrhizobium hipponense	strain=aSej3	GCA_008123965.1	2605638	2605638	type	True	76.2184	61	551	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	76.1914	60	551	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	76.1821	63	551	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	76.1339	81	551	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.1222	66	551	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.1212	55	551	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	76.0488	58	551	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	76.0089	58	551	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.9276	69	551	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:13:29,821] [INFO] DFAST Taxonomy check result was written to GCA_947484455.1_TH-Jun18-202_genomic.fna/tc_result.tsv
[2023-06-13 18:13:29,821] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:13:29,821] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:13:29,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4929c480-93eb-40bf-a519-f4015ffdd94f/dqc_reference/checkm_data
[2023-06-13 18:13:29,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:13:29,846] [INFO] Task started: CheckM
[2023-06-13 18:13:29,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947484455.1_TH-Jun18-202_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947484455.1_TH-Jun18-202_genomic.fna/checkm_input GCA_947484455.1_TH-Jun18-202_genomic.fna/checkm_result
[2023-06-13 18:13:47,361] [INFO] Task succeeded: CheckM
[2023-06-13 18:13:47,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:13:47,383] [INFO] ===== Completeness check finished =====
[2023-06-13 18:13:47,383] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:13:47,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947484455.1_TH-Jun18-202_genomic.fna/markers.fasta)
[2023-06-13 18:13:47,384] [INFO] Task started: Blastn
[2023-06-13 18:13:47,384] [INFO] Running command: blastn -query GCA_947484455.1_TH-Jun18-202_genomic.fna/markers.fasta -db /var/lib/cwl/stg4929c480-93eb-40bf-a519-f4015ffdd94f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947484455.1_TH-Jun18-202_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:13:48,286] [INFO] Task succeeded: Blastn
[2023-06-13 18:13:48,289] [INFO] Selected 7 target genomes.
[2023-06-13 18:13:48,289] [INFO] Target genome list was writen to GCA_947484455.1_TH-Jun18-202_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:13:48,290] [INFO] Task started: fastANI
[2023-06-13 18:13:48,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d451878-354c-44b4-9177-45773d60e344/GCA_947484455.1_TH-Jun18-202_genomic.fna.gz --refList GCA_947484455.1_TH-Jun18-202_genomic.fna/target_genomes_gtdb.txt --output GCA_947484455.1_TH-Jun18-202_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:13:52,900] [INFO] Task succeeded: fastANI
[2023-06-13 18:13:52,906] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 18:13:52,907] [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_903831485.1	s__UBA7672 sp903831485	97.103	402	551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903842595.1	s__UBA7672 sp903842595	87.4459	500	551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280725.1	s__UBA7672 sp002280725	80.5543	383	551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483135.1	s__UBA7672 sp002483135	80.1232	370	551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714495.1	s__UBA7672 sp016714495	79.413	323	551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125405.1	s__UBA7672 sp016125405	77.9471	201	551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792365.1	s__IH12 sp017792365	77.6592	141	551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__IH12	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 18:13:52,909] [INFO] GTDB search result was written to GCA_947484455.1_TH-Jun18-202_genomic.fna/result_gtdb.tsv
[2023-06-13 18:13:52,910] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:13:52,913] [INFO] DFAST_QC result json was written to GCA_947484455.1_TH-Jun18-202_genomic.fna/dqc_result.json
[2023-06-13 18:13:52,913] [INFO] DFAST_QC completed!
[2023-06-13 18:13:52,913] [INFO] Total running time: 0h0m45s