[2024-01-25 19:42:20,864] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:20,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:20,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg1131a361-a452-48d3-a31d-8cf1057aa023/dqc_reference
[2024-01-25 19:42:22,114] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:22,115] [INFO] Task started: Prodigal
[2024-01-25 19:42:22,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a15ade3-d2bd-48d0-b83d-c38f7bf7ddd2/GCF_014635705.1_ASM1463570v1_genomic.fna.gz | prodigal -d GCF_014635705.1_ASM1463570v1_genomic.fna/cds.fna -a GCF_014635705.1_ASM1463570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:32,285] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:32,285] [INFO] Task started: HMMsearch
[2024-01-25 19:42:32,285] [INFO] Running command: hmmsearch --tblout GCF_014635705.1_ASM1463570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1131a361-a452-48d3-a31d-8cf1057aa023/dqc_reference/reference_markers.hmm GCF_014635705.1_ASM1463570v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:32,520] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:32,521] [INFO] Found 6/6 markers.
[2024-01-25 19:42:32,548] [INFO] Query marker FASTA was written to GCF_014635705.1_ASM1463570v1_genomic.fna/markers.fasta
[2024-01-25 19:42:32,548] [INFO] Task started: Blastn
[2024-01-25 19:42:32,548] [INFO] Running command: blastn -query GCF_014635705.1_ASM1463570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1131a361-a452-48d3-a31d-8cf1057aa023/dqc_reference/reference_markers.fasta -out GCF_014635705.1_ASM1463570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:33,298] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:33,301] [INFO] Selected 21 target genomes.
[2024-01-25 19:42:33,301] [INFO] Target genome list was writen to GCF_014635705.1_ASM1463570v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:33,310] [INFO] Task started: fastANI
[2024-01-25 19:42:33,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a15ade3-d2bd-48d0-b83d-c38f7bf7ddd2/GCF_014635705.1_ASM1463570v1_genomic.fna.gz --refList GCF_014635705.1_ASM1463570v1_genomic.fna/target_genomes.txt --output GCF_014635705.1_ASM1463570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:51,169] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:51,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1131a361-a452-48d3-a31d-8cf1057aa023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:51,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1131a361-a452-48d3-a31d-8cf1057aa023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:51,194] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:51,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:51,195] [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
Oxalicibacterium faecigallinarum	strain=CCM 2767	GCA_014635705.1	573741	573741	type	True	100.0	1102	1104	95	conclusive
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	80.3875	569	1104	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	79.2395	430	1104	95	below_threshold
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	78.931	394	1104	95	below_threshold
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	78.8782	401	1104	95	below_threshold
Herminiimonas arsenitoxidans	strain=AS8	GCA_900130075.1	1809410	1809410	type	True	78.8115	398	1104	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	78.3378	257	1104	95	below_threshold
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	78.1905	260	1104	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	78.0486	232	1104	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	78.0454	235	1104	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	78.0294	251	1104	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	78.0226	220	1104	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	77.9959	235	1104	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	77.9598	266	1104	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	77.8676	234	1104	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	77.8468	254	1104	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	77.813	253	1104	95	below_threshold
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	77.4972	246	1104	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	77.4633	208	1104	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	77.4126	193	1104	95	below_threshold
Glaciimonas soli	strain=GS1	GCA_009497155.1	2590999	2590999	type	True	77.1399	94	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:51,196] [INFO] DFAST Taxonomy check result was written to GCF_014635705.1_ASM1463570v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:51,197] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:51,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:51,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1131a361-a452-48d3-a31d-8cf1057aa023/dqc_reference/checkm_data
[2024-01-25 19:42:51,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:51,257] [INFO] Task started: CheckM
[2024-01-25 19:42:51,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635705.1_ASM1463570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635705.1_ASM1463570v1_genomic.fna/checkm_input GCF_014635705.1_ASM1463570v1_genomic.fna/checkm_result
[2024-01-25 19:43:25,271] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:25,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:25,286] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:25,286] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:25,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635705.1_ASM1463570v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:25,287] [INFO] Task started: Blastn
[2024-01-25 19:43:25,287] [INFO] Running command: blastn -query GCF_014635705.1_ASM1463570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1131a361-a452-48d3-a31d-8cf1057aa023/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635705.1_ASM1463570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:26,598] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:26,601] [INFO] Selected 19 target genomes.
[2024-01-25 19:43:26,601] [INFO] Target genome list was writen to GCF_014635705.1_ASM1463570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:26,633] [INFO] Task started: fastANI
[2024-01-25 19:43:26,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a15ade3-d2bd-48d0-b83d-c38f7bf7ddd2/GCF_014635705.1_ASM1463570v1_genomic.fna.gz --refList GCF_014635705.1_ASM1463570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635705.1_ASM1463570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:41,676] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:41,688] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:41,688] [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_014635705.1	s__Oxalicibacterium faecigallinarum	100.0	1102	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014635065.1	s__Oxalicibacterium flavum	80.3978	568	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635845.1	s__Oxalicibacterium solurbis	79.2395	430	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000026125.1	s__Herminiimonas arsenicoxydans	79.0321	427	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013625.1	s__Herminiimonas sp000013625	78.8956	401	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293745.1	s__Herminiimonas fonticola	78.8782	401	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015645465.1	s__Herminiimonas contaminans	78.8661	398	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	97.73	97.73	0.94	0.94	3	-
GCF_003852535.1	s__Herminiimonas sp003852535	78.8468	426	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464355.1	s__Herminiimonas sp001464355	78.594	397	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384815.1	s__Herminiimonas sp002384815	78.4633	373	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	78.3228	258	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267925.1	s__Herbaspirillum hiltneri	78.2633	261	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.60	97.60	0.89	0.89	2	-
GCF_000256565.1	s__Herbaspirillum lusitanum	78.0641	231	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018305005.1	s__Collimonas sp018305005	77.8827	233	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	77.8422	246	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584185.1	s__Collimonas pratensis	77.7531	253	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_002564105.1	s__Collimonas sp002564105	77.673	239	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	77.4972	246	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009497155.1	s__Glaciimonas soli	77.1399	94	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:41,690] [INFO] GTDB search result was written to GCF_014635705.1_ASM1463570v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:41,690] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:41,694] [INFO] DFAST_QC result json was written to GCF_014635705.1_ASM1463570v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:41,694] [INFO] DFAST_QC completed!
[2024-01-25 19:43:41,694] [INFO] Total running time: 0h1m21s