[2023-06-08 12:36:52,618] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:36:52,620] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:36:52,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg6beb2fb8-7039-4041-b4e1-ed4483fa4574/dqc_reference
[2023-06-08 12:36:53,940] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:36:53,941] [INFO] Task started: Prodigal
[2023-06-08 12:36:53,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg09effb19-4952-4564-b15c-bf8e03caeab3/GCA_947451565.1_Jr-20nov17-27_genomic.fna.gz | prodigal -d GCA_947451565.1_Jr-20nov17-27_genomic.fna/cds.fna -a GCA_947451565.1_Jr-20nov17-27_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:37:02,015] [INFO] Task succeeded: Prodigal
[2023-06-08 12:37:02,015] [INFO] Task started: HMMsearch
[2023-06-08 12:37:02,015] [INFO] Running command: hmmsearch --tblout GCA_947451565.1_Jr-20nov17-27_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6beb2fb8-7039-4041-b4e1-ed4483fa4574/dqc_reference/reference_markers.hmm GCA_947451565.1_Jr-20nov17-27_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:37:02,242] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:37:02,243] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg09effb19-4952-4564-b15c-bf8e03caeab3/GCA_947451565.1_Jr-20nov17-27_genomic.fna.gz]
[2023-06-08 12:37:02,268] [INFO] Query marker FASTA was written to GCA_947451565.1_Jr-20nov17-27_genomic.fna/markers.fasta
[2023-06-08 12:37:02,268] [INFO] Task started: Blastn
[2023-06-08 12:37:02,269] [INFO] Running command: blastn -query GCA_947451565.1_Jr-20nov17-27_genomic.fna/markers.fasta -db /var/lib/cwl/stg6beb2fb8-7039-4041-b4e1-ed4483fa4574/dqc_reference/reference_markers.fasta -out GCA_947451565.1_Jr-20nov17-27_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:37:02,823] [INFO] Task succeeded: Blastn
[2023-06-08 12:37:02,827] [INFO] Selected 8 target genomes.
[2023-06-08 12:37:02,827] [INFO] Target genome list was writen to GCA_947451565.1_Jr-20nov17-27_genomic.fna/target_genomes.txt
[2023-06-08 12:37:02,828] [INFO] Task started: fastANI
[2023-06-08 12:37:02,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg09effb19-4952-4564-b15c-bf8e03caeab3/GCA_947451565.1_Jr-20nov17-27_genomic.fna.gz --refList GCA_947451565.1_Jr-20nov17-27_genomic.fna/target_genomes.txt --output GCA_947451565.1_Jr-20nov17-27_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:37:08,824] [INFO] Task succeeded: fastANI
[2023-06-08 12:37:08,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6beb2fb8-7039-4041-b4e1-ed4483fa4574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:37:08,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6beb2fb8-7039-4041-b4e1-ed4483fa4574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:37:08,833] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:37:08,833] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:37:08,833] [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
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	86.0848	489	640	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	77.9988	196	640	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.1183	125	640	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.0326	133	640	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	76.7202	87	640	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	76.662	128	640	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	76.1869	104	640	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:37:08,836] [INFO] DFAST Taxonomy check result was written to GCA_947451565.1_Jr-20nov17-27_genomic.fna/tc_result.tsv
[2023-06-08 12:37:08,836] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:37:08,836] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:37:08,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6beb2fb8-7039-4041-b4e1-ed4483fa4574/dqc_reference/checkm_data
[2023-06-08 12:37:08,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:37:08,869] [INFO] Task started: CheckM
[2023-06-08 12:37:08,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947451565.1_Jr-20nov17-27_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947451565.1_Jr-20nov17-27_genomic.fna/checkm_input GCA_947451565.1_Jr-20nov17-27_genomic.fna/checkm_result
[2023-06-08 12:37:37,897] [INFO] Task succeeded: CheckM
[2023-06-08 12:37:37,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 21.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:37:37,919] [INFO] ===== Completeness check finished =====
[2023-06-08 12:37:37,920] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:37:37,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947451565.1_Jr-20nov17-27_genomic.fna/markers.fasta)
[2023-06-08 12:37:37,920] [INFO] Task started: Blastn
[2023-06-08 12:37:37,921] [INFO] Running command: blastn -query GCA_947451565.1_Jr-20nov17-27_genomic.fna/markers.fasta -db /var/lib/cwl/stg6beb2fb8-7039-4041-b4e1-ed4483fa4574/dqc_reference/reference_markers_gtdb.fasta -out GCA_947451565.1_Jr-20nov17-27_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:37:38,545] [INFO] Task succeeded: Blastn
[2023-06-08 12:37:38,549] [INFO] Selected 8 target genomes.
[2023-06-08 12:37:38,550] [INFO] Target genome list was writen to GCA_947451565.1_Jr-20nov17-27_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:37:38,552] [INFO] Task started: fastANI
[2023-06-08 12:37:38,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg09effb19-4952-4564-b15c-bf8e03caeab3/GCA_947451565.1_Jr-20nov17-27_genomic.fna.gz --refList GCA_947451565.1_Jr-20nov17-27_genomic.fna/target_genomes_gtdb.txt --output GCA_947451565.1_Jr-20nov17-27_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:37:43,222] [INFO] Task succeeded: fastANI
[2023-06-08 12:37:43,234] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:37:43,234] [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_003063475.1	s__Limnohabitans curvus	86.0848	489	640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.49	98.49	0.87	0.87	2	-
GCA_002282445.1	s__Limnohabitans sp002282445	84.5344	412	640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	100.00	100.00	0.99	0.99	3	-
GCF_003063545.1	s__Limnohabitans sp003063545	84.4486	439	640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886485.1	s__Limnohabitans sp903886485	83.6516	475	640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.98	99.98	0.98	0.98	3	-
GCA_903952885.1	s__Limnohabitans sp903952885	82.8337	324	640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.13	99.13	0.83	0.83	2	-
GCF_002778325.1	s__Limnohabitans sp002778325	82.0827	392	640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897925.1	s__Rhodoferax sp903897925	76.6947	89	640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.65	99.65	0.87	0.87	2	-
GCF_014109725.1	s__Comamonas piscis	76.2875	91	640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:37:43,236] [INFO] GTDB search result was written to GCA_947451565.1_Jr-20nov17-27_genomic.fna/result_gtdb.tsv
[2023-06-08 12:37:43,237] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:37:43,240] [INFO] DFAST_QC result json was written to GCA_947451565.1_Jr-20nov17-27_genomic.fna/dqc_result.json
[2023-06-08 12:37:43,240] [INFO] DFAST_QC completed!
[2023-06-08 12:37:43,240] [INFO] Total running time: 0h0m51s