[2024-01-24 12:21:59,159] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:59,161] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:59,161] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b539715-9e85-42cf-87ed-849e5d314cf2/dqc_reference
[2024-01-24 12:22:00,565] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:00,566] [INFO] Task started: Prodigal
[2024-01-24 12:22:00,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f65b8b5-5cd1-49ea-ad8a-f8f88f639f41/GCF_004363315.1_ASM436331v1_genomic.fna.gz | prodigal -d GCF_004363315.1_ASM436331v1_genomic.fna/cds.fna -a GCF_004363315.1_ASM436331v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:10,965] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:10,965] [INFO] Task started: HMMsearch
[2024-01-24 12:22:10,965] [INFO] Running command: hmmsearch --tblout GCF_004363315.1_ASM436331v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b539715-9e85-42cf-87ed-849e5d314cf2/dqc_reference/reference_markers.hmm GCF_004363315.1_ASM436331v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:11,313] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:11,314] [INFO] Found 6/6 markers.
[2024-01-24 12:22:11,360] [INFO] Query marker FASTA was written to GCF_004363315.1_ASM436331v1_genomic.fna/markers.fasta
[2024-01-24 12:22:11,360] [INFO] Task started: Blastn
[2024-01-24 12:22:11,361] [INFO] Running command: blastn -query GCF_004363315.1_ASM436331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b539715-9e85-42cf-87ed-849e5d314cf2/dqc_reference/reference_markers.fasta -out GCF_004363315.1_ASM436331v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:12,273] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:12,275] [INFO] Selected 21 target genomes.
[2024-01-24 12:22:12,276] [INFO] Target genome list was writen to GCF_004363315.1_ASM436331v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:12,283] [INFO] Task started: fastANI
[2024-01-24 12:22:12,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f65b8b5-5cd1-49ea-ad8a-f8f88f639f41/GCF_004363315.1_ASM436331v1_genomic.fna.gz --refList GCF_004363315.1_ASM436331v1_genomic.fna/target_genomes.txt --output GCF_004363315.1_ASM436331v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:26,601] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:26,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b539715-9e85-42cf-87ed-849e5d314cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:26,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b539715-9e85-42cf-87ed-849e5d314cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:26,618] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:26,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:26,618] [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
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	84.4328	683	913	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	82.1062	536	913	95	below_threshold
Tepidimonas aquatica	strain=CLN-1	GCA_007556585.1	247482	247482	type	True	81.0611	459	913	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	80.7472	477	913	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	80.7069	492	913	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	80.6785	487	913	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	80.6674	494	913	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	80.2921	503	913	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.1699	508	913	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	80.1498	488	913	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	80.0509	484	913	95	below_threshold
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	79.9373	447	913	95	below_threshold
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	79.8894	454	913	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	79.8809	431	913	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	79.7525	413	913	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	79.4902	427	913	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.4841	388	913	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	79.0586	413	913	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.8113	408	913	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.768	350	913	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.7076	418	913	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:26,623] [INFO] DFAST Taxonomy check result was written to GCF_004363315.1_ASM436331v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:26,624] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:26,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:26,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b539715-9e85-42cf-87ed-849e5d314cf2/dqc_reference/checkm_data
[2024-01-24 12:22:26,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:26,654] [INFO] Task started: CheckM
[2024-01-24 12:22:26,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363315.1_ASM436331v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363315.1_ASM436331v1_genomic.fna/checkm_input GCF_004363315.1_ASM436331v1_genomic.fna/checkm_result
[2024-01-24 12:23:10,386] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:10,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:10,410] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:10,411] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:10,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363315.1_ASM436331v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:10,412] [INFO] Task started: Blastn
[2024-01-24 12:23:10,412] [INFO] Running command: blastn -query GCF_004363315.1_ASM436331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b539715-9e85-42cf-87ed-849e5d314cf2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363315.1_ASM436331v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:12,172] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:12,175] [INFO] Selected 14 target genomes.
[2024-01-24 12:23:12,175] [INFO] Target genome list was writen to GCF_004363315.1_ASM436331v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:12,185] [INFO] Task started: fastANI
[2024-01-24 12:23:12,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f65b8b5-5cd1-49ea-ad8a-f8f88f639f41/GCF_004363315.1_ASM436331v1_genomic.fna.gz --refList GCF_004363315.1_ASM436331v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363315.1_ASM436331v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:21,364] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:21,379] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:21,380] [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_004363315.1	s__Tepidicella xavieri	100.0	910	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013432195.1	s__Tepidicella baoligensis	84.4328	683	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	82.4078	547	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	82.0515	539	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCA_002291945.1	s__UBA997 sp002291945	81.2449	450	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA997	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556705.1	s__Tepidimonas thermarum	80.7054	495	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837135.1	s__Macromonas bipunctata	80.1388	387	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693755.1	s__Tibeticola sp013693755	80.0488	452	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_000828915.1	s__Serpentinomonas mccroryi	79.9654	443	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	98.21	97.99	0.96	0.95	3	-
GCF_000828895.1	s__Serpentinomonas raichei	79.8891	454	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696225.1	s__Serpentinomonas sp000696225	79.8675	432	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980625.1	s__Malikia spinosa	79.7717	409	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	97.79	97.60	0.88	0.88	3	-
GCF_004681965.1	s__Ramlibacter rhizophilus	79.5095	425	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745855.1	s__Xenophilus azovorans	79.3821	450	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:21,382] [INFO] GTDB search result was written to GCF_004363315.1_ASM436331v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:21,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:21,390] [INFO] DFAST_QC result json was written to GCF_004363315.1_ASM436331v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:21,390] [INFO] DFAST_QC completed!
[2024-01-24 12:23:21,391] [INFO] Total running time: 0h1m22s