[2024-01-24 11:51:24,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg33d53971-52ff-4a8d-adaa-1ddc08fdbc37/dqc_reference
[2024-01-24 11:51:25,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,903] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,903] [INFO] Running command: gunzip -c /var/lib/cwl/stgf754e294-9e19-46e5-ac68-61d0a4fff178/GCF_000154705.2_ASM15470v2_genomic.fna.gz | prodigal -d GCF_000154705.2_ASM15470v2_genomic.fna/cds.fna -a GCF_000154705.2_ASM15470v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:40,765] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:40,766] [INFO] Task started: HMMsearch
[2024-01-24 11:51:40,766] [INFO] Running command: hmmsearch --tblout GCF_000154705.2_ASM15470v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33d53971-52ff-4a8d-adaa-1ddc08fdbc37/dqc_reference/reference_markers.hmm GCF_000154705.2_ASM15470v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:41,061] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:41,063] [INFO] Found 6/6 markers.
[2024-01-24 11:51:41,105] [INFO] Query marker FASTA was written to GCF_000154705.2_ASM15470v2_genomic.fna/markers.fasta
[2024-01-24 11:51:41,105] [INFO] Task started: Blastn
[2024-01-24 11:51:41,105] [INFO] Running command: blastn -query GCF_000154705.2_ASM15470v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg33d53971-52ff-4a8d-adaa-1ddc08fdbc37/dqc_reference/reference_markers.fasta -out GCF_000154705.2_ASM15470v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:42,095] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:42,098] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:42,099] [INFO] Target genome list was writen to GCF_000154705.2_ASM15470v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:42,104] [INFO] Task started: fastANI
[2024-01-24 11:51:42,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgf754e294-9e19-46e5-ac68-61d0a4fff178/GCF_000154705.2_ASM15470v2_genomic.fna.gz --refList GCF_000154705.2_ASM15470v2_genomic.fna/target_genomes.txt --output GCF_000154705.2_ASM15470v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:52,429] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:52,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33d53971-52ff-4a8d-adaa-1ddc08fdbc37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:52,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33d53971-52ff-4a8d-adaa-1ddc08fdbc37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:52,439] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:52,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:52,439] [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 phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	100.0	1488	1489	95	conclusive
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	81.1527	901	1489	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	80.6358	813	1489	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	80.4004	778	1489	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.2496	582	1489	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	77.9984	333	1489	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.9519	312	1489	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.8187	343	1489	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.5666	308	1489	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.5565	336	1489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:52,441] [INFO] DFAST Taxonomy check result was written to GCF_000154705.2_ASM15470v2_genomic.fna/tc_result.tsv
[2024-01-24 11:51:52,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:52,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:52,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33d53971-52ff-4a8d-adaa-1ddc08fdbc37/dqc_reference/checkm_data
[2024-01-24 11:51:52,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:52,484] [INFO] Task started: CheckM
[2024-01-24 11:51:52,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000154705.2_ASM15470v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000154705.2_ASM15470v2_genomic.fna/checkm_input GCF_000154705.2_ASM15470v2_genomic.fna/checkm_result
[2024-01-24 11:52:46,674] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:46,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:46,699] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:46,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:46,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000154705.2_ASM15470v2_genomic.fna/markers.fasta)
[2024-01-24 11:52:46,700] [INFO] Task started: Blastn
[2024-01-24 11:52:46,700] [INFO] Running command: blastn -query GCF_000154705.2_ASM15470v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg33d53971-52ff-4a8d-adaa-1ddc08fdbc37/dqc_reference/reference_markers_gtdb.fasta -out GCF_000154705.2_ASM15470v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:48,624] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:48,627] [INFO] Selected 9 target genomes.
[2024-01-24 11:52:48,628] [INFO] Target genome list was writen to GCF_000154705.2_ASM15470v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:48,657] [INFO] Task started: fastANI
[2024-01-24 11:52:48,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgf754e294-9e19-46e5-ac68-61d0a4fff178/GCF_000154705.2_ASM15470v2_genomic.fna.gz --refList GCF_000154705.2_ASM15470v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000154705.2_ASM15470v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:58,165] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:58,180] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:58,180] [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_000154705.2	s__Hoeflea phototrophica	100.0	1488	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018829385.1	s__Hoeflea sp018829385	81.457	514	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498795.1	s__Hoeflea sp902498795	81.417	859	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCA_002733955.1	s__Hoeflea sp002733955	81.2379	830	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359905.1	s__Hoeflea sp014359905	81.0825	783	1489	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	81.0103	804	1489	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	80.8797	815	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_001703635.1	s__Hoeflea olei	80.6353	813	1489	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	80.4116	777	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:58,182] [INFO] GTDB search result was written to GCF_000154705.2_ASM15470v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:58,182] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:58,185] [INFO] DFAST_QC result json was written to GCF_000154705.2_ASM15470v2_genomic.fna/dqc_result.json
[2024-01-24 11:52:58,185] [INFO] DFAST_QC completed!
[2024-01-24 11:52:58,185] [INFO] Total running time: 0h1m34s