[2024-01-24 13:48:56,791] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:56,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:56,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg67cb5350-f51c-49fd-a9e4-dda73b354f96/dqc_reference
[2024-01-24 13:48:58,032] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:58,033] [INFO] Task started: Prodigal
[2024-01-24 13:48:58,033] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ae17de1-8cc6-4dff-8e46-72da3b3d91b9/GCF_007556615.1_ASM755661v1_genomic.fna.gz | prodigal -d GCF_007556615.1_ASM755661v1_genomic.fna/cds.fna -a GCF_007556615.1_ASM755661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:08,419] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:08,419] [INFO] Task started: HMMsearch
[2024-01-24 13:49:08,419] [INFO] Running command: hmmsearch --tblout GCF_007556615.1_ASM755661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67cb5350-f51c-49fd-a9e4-dda73b354f96/dqc_reference/reference_markers.hmm GCF_007556615.1_ASM755661v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:08,692] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:08,693] [INFO] Found 6/6 markers.
[2024-01-24 13:49:08,721] [INFO] Query marker FASTA was written to GCF_007556615.1_ASM755661v1_genomic.fna/markers.fasta
[2024-01-24 13:49:08,721] [INFO] Task started: Blastn
[2024-01-24 13:49:08,721] [INFO] Running command: blastn -query GCF_007556615.1_ASM755661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67cb5350-f51c-49fd-a9e4-dda73b354f96/dqc_reference/reference_markers.fasta -out GCF_007556615.1_ASM755661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:09,753] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:09,757] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:09,758] [INFO] Target genome list was writen to GCF_007556615.1_ASM755661v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:09,764] [INFO] Task started: fastANI
[2024-01-24 13:49:09,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ae17de1-8cc6-4dff-8e46-72da3b3d91b9/GCF_007556615.1_ASM755661v1_genomic.fna.gz --refList GCF_007556615.1_ASM755661v1_genomic.fna/target_genomes.txt --output GCF_007556615.1_ASM755661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:19,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:19,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67cb5350-f51c-49fd-a9e4-dda73b354f96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:19,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67cb5350-f51c-49fd-a9e4-dda73b354f96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:19,097] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:19,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:19,097] [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
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	100.0	881	887	95	conclusive
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	99.992	864	887	95	conclusive
Tepidimonas aquatica	strain=CLN-1	GCA_007556585.1	247482	247482	type	True	94.233	716	887	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	85.2785	680	887	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	84.0004	638	887	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	83.9603	615	887	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	83.6691	626	887	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.7315	478	887	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.7505	446	887	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.6317	410	887	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.4707	364	887	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.1932	358	887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:19,099] [INFO] DFAST Taxonomy check result was written to GCF_007556615.1_ASM755661v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:19,099] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:19,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:19,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67cb5350-f51c-49fd-a9e4-dda73b354f96/dqc_reference/checkm_data
[2024-01-24 13:49:19,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:19,133] [INFO] Task started: CheckM
[2024-01-24 13:49:19,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007556615.1_ASM755661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007556615.1_ASM755661v1_genomic.fna/checkm_input GCF_007556615.1_ASM755661v1_genomic.fna/checkm_result
[2024-01-24 13:50:07,852] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:07,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:07,871] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:07,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:07,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007556615.1_ASM755661v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:07,872] [INFO] Task started: Blastn
[2024-01-24 13:50:07,872] [INFO] Running command: blastn -query GCF_007556615.1_ASM755661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67cb5350-f51c-49fd-a9e4-dda73b354f96/dqc_reference/reference_markers_gtdb.fasta -out GCF_007556615.1_ASM755661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:09,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:09,724] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:09,724] [INFO] Target genome list was writen to GCF_007556615.1_ASM755661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:09,752] [INFO] Task started: fastANI
[2024-01-24 13:50:09,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ae17de1-8cc6-4dff-8e46-72da3b3d91b9/GCF_007556615.1_ASM755661v1_genomic.fna.gz --refList GCF_007556615.1_ASM755661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007556615.1_ASM755661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:22,675] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:22,689] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:22,689] [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_004342625.1	s__Tepidimonas ignava	99.992	864	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_007556585.1	s__Tepidimonas aquatica	94.2542	715	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556605.1	s__Tepidimonas sediminis	85.2945	679	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	83.9992	636	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCF_007556595.1	s__Tepidimonas alkaliphilus	83.9663	614	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556705.1	s__Tepidimonas thermarum	83.6407	627	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556685.1	s__Tepidimonas charontis	82.9786	602	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015159745.1	s__Ramlibacter aquaticus	79.0817	418	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:22,691] [INFO] GTDB search result was written to GCF_007556615.1_ASM755661v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:22,691] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:22,694] [INFO] DFAST_QC result json was written to GCF_007556615.1_ASM755661v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:22,694] [INFO] DFAST_QC completed!
[2024-01-24 13:50:22,694] [INFO] Total running time: 0h1m26s