[2024-01-25 19:51:50,759] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:50,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:50,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a0f2507-e68c-44e3-89a3-5b7ba91cf877/dqc_reference
[2024-01-25 19:51:52,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:52,006] [INFO] Task started: Prodigal
[2024-01-25 19:51:52,006] [INFO] Running command: gunzip -c /var/lib/cwl/stg5039cb69-a570-483c-9e53-868e481f4bec/GCF_026619425.1_ASM2661942v1_genomic.fna.gz | prodigal -d GCF_026619425.1_ASM2661942v1_genomic.fna/cds.fna -a GCF_026619425.1_ASM2661942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:06,387] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:06,387] [INFO] Task started: HMMsearch
[2024-01-25 19:52:06,387] [INFO] Running command: hmmsearch --tblout GCF_026619425.1_ASM2661942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a0f2507-e68c-44e3-89a3-5b7ba91cf877/dqc_reference/reference_markers.hmm GCF_026619425.1_ASM2661942v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:06,662] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:06,663] [INFO] Found 6/6 markers.
[2024-01-25 19:52:06,705] [INFO] Query marker FASTA was written to GCF_026619425.1_ASM2661942v1_genomic.fna/markers.fasta
[2024-01-25 19:52:06,705] [INFO] Task started: Blastn
[2024-01-25 19:52:06,705] [INFO] Running command: blastn -query GCF_026619425.1_ASM2661942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a0f2507-e68c-44e3-89a3-5b7ba91cf877/dqc_reference/reference_markers.fasta -out GCF_026619425.1_ASM2661942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:07,674] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:07,677] [INFO] Selected 11 target genomes.
[2024-01-25 19:52:07,677] [INFO] Target genome list was writen to GCF_026619425.1_ASM2661942v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:07,696] [INFO] Task started: fastANI
[2024-01-25 19:52:07,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg5039cb69-a570-483c-9e53-868e481f4bec/GCF_026619425.1_ASM2661942v1_genomic.fna.gz --refList GCF_026619425.1_ASM2661942v1_genomic.fna/target_genomes.txt --output GCF_026619425.1_ASM2661942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:19,702] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:19,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a0f2507-e68c-44e3-89a3-5b7ba91cf877/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:19,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a0f2507-e68c-44e3-89a3-5b7ba91cf877/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:19,711] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:52:19,711] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:19,711] [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
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	99.889	1634	1684	95	conclusive
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	82.6272	1027	1684	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	82.0065	946	1684	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	81.2302	900	1684	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.8356	740	1684	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.4063	468	1684	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	78.3777	445	1684	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	78.1383	504	1684	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.1039	499	1684	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.9029	386	1684	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.9018	345	1684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:19,713] [INFO] DFAST Taxonomy check result was written to GCF_026619425.1_ASM2661942v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:19,713] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:19,713] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:19,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a0f2507-e68c-44e3-89a3-5b7ba91cf877/dqc_reference/checkm_data
[2024-01-25 19:52:19,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:19,766] [INFO] Task started: CheckM
[2024-01-25 19:52:19,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026619425.1_ASM2661942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026619425.1_ASM2661942v1_genomic.fna/checkm_input GCF_026619425.1_ASM2661942v1_genomic.fna/checkm_result
[2024-01-25 19:53:11,030] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:11,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:11,048] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:11,049] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:11,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026619425.1_ASM2661942v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:11,049] [INFO] Task started: Blastn
[2024-01-25 19:53:11,049] [INFO] Running command: blastn -query GCF_026619425.1_ASM2661942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a0f2507-e68c-44e3-89a3-5b7ba91cf877/dqc_reference/reference_markers_gtdb.fasta -out GCF_026619425.1_ASM2661942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:12,959] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:12,962] [INFO] Selected 11 target genomes.
[2024-01-25 19:53:12,962] [INFO] Target genome list was writen to GCF_026619425.1_ASM2661942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:12,971] [INFO] Task started: fastANI
[2024-01-25 19:53:12,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg5039cb69-a570-483c-9e53-868e481f4bec/GCF_026619425.1_ASM2661942v1_genomic.fna.gz --refList GCF_026619425.1_ASM2661942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026619425.1_ASM2661942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:25,172] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:25,180] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:25,180] [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_902498795.1	s__Hoeflea sp902498795	97.8889	1496	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	conclusive
GCA_018829385.1	s__Hoeflea sp018829385	86.3789	724	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733955.1	s__Hoeflea sp002733955	83.7018	1159	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759435.1	s__Hoeflea sp000759435	83.1295	1032	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220985.1	s__Hoeflea halophila	82.6272	1027	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084245.1	s__Hoeflea sp019084245	82.5493	1048	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCA_014359905.1	s__Hoeflea sp014359905	82.4402	978	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961635.1	s__Hoeflea sp000961635	82.1465	642	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001703635.1	s__Hoeflea olei	82.0172	945	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001011155.1	s__Hoeflea sp001011155	81.4672	950	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154705.2	s__Hoeflea phototrophica	81.2402	897	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:25,181] [INFO] GTDB search result was written to GCF_026619425.1_ASM2661942v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:25,182] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:25,185] [INFO] DFAST_QC result json was written to GCF_026619425.1_ASM2661942v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:25,185] [INFO] DFAST_QC completed!
[2024-01-25 19:53:25,185] [INFO] Total running time: 0h1m34s