[2024-01-24 12:30:05,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,383] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe7e1ffa-55c7-496d-8724-eeeef08b0847/dqc_reference
[2024-01-24 12:30:07,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,249] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,250] [INFO] Running command: gunzip -c /var/lib/cwl/stgecae6efb-0b7a-4b95-a43c-478f29edb5de/GCF_014489575.1_ASM1448957v1_genomic.fna.gz | prodigal -d GCF_014489575.1_ASM1448957v1_genomic.fna/cds.fna -a GCF_014489575.1_ASM1448957v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:17,464] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:17,464] [INFO] Task started: HMMsearch
[2024-01-24 12:30:17,464] [INFO] Running command: hmmsearch --tblout GCF_014489575.1_ASM1448957v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe7e1ffa-55c7-496d-8724-eeeef08b0847/dqc_reference/reference_markers.hmm GCF_014489575.1_ASM1448957v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:17,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:17,801] [INFO] Found 6/6 markers.
[2024-01-24 12:30:17,845] [INFO] Query marker FASTA was written to GCF_014489575.1_ASM1448957v1_genomic.fna/markers.fasta
[2024-01-24 12:30:17,845] [INFO] Task started: Blastn
[2024-01-24 12:30:17,845] [INFO] Running command: blastn -query GCF_014489575.1_ASM1448957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe7e1ffa-55c7-496d-8724-eeeef08b0847/dqc_reference/reference_markers.fasta -out GCF_014489575.1_ASM1448957v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:18,951] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:18,954] [INFO] Selected 12 target genomes.
[2024-01-24 12:30:18,954] [INFO] Target genome list was writen to GCF_014489575.1_ASM1448957v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:18,958] [INFO] Task started: fastANI
[2024-01-24 12:30:18,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgecae6efb-0b7a-4b95-a43c-478f29edb5de/GCF_014489575.1_ASM1448957v1_genomic.fna.gz --refList GCF_014489575.1_ASM1448957v1_genomic.fna/target_genomes.txt --output GCF_014489575.1_ASM1448957v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:28,103] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:28,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe7e1ffa-55c7-496d-8724-eeeef08b0847/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:28,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe7e1ffa-55c7-496d-8724-eeeef08b0847/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:28,112] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:28,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:28,112] [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
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	100.0	1288	1288	95	conclusive
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	81.7526	612	1288	95	below_threshold
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	81.7248	678	1288	95	below_threshold
Tessaracoccus aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	81.4141	656	1288	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	81.1646	558	1288	95	below_threshold
Tessaracoccus bendigoensis	strain=DSM 12906	GCA_900141915.1	72764	72764	type	True	80.5129	520	1288	95	below_threshold
Tessaracoccus flavus	strain=RP1	GCA_001997295.1	1610493	1610493	type	True	80.4929	483	1288	95	below_threshold
Tessaracoccus flavus	strain=RP1	GCA_900107385.1	1610493	1610493	type	True	80.372	481	1288	95	below_threshold
Tessaracoccus oleiagri	strain=CGMCC 1.9159	GCA_900103275.1	686624	686624	type	True	79.2286	433	1288	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	78.373	322	1288	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.0525	219	1288	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.9734	326	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:28,115] [INFO] DFAST Taxonomy check result was written to GCF_014489575.1_ASM1448957v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:28,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:28,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:28,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe7e1ffa-55c7-496d-8724-eeeef08b0847/dqc_reference/checkm_data
[2024-01-24 12:30:28,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:28,157] [INFO] Task started: CheckM
[2024-01-24 12:30:28,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014489575.1_ASM1448957v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014489575.1_ASM1448957v1_genomic.fna/checkm_input GCF_014489575.1_ASM1448957v1_genomic.fna/checkm_result
[2024-01-24 12:31:08,753] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:08,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:08,780] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:08,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:08,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014489575.1_ASM1448957v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:08,781] [INFO] Task started: Blastn
[2024-01-24 12:31:08,781] [INFO] Running command: blastn -query GCF_014489575.1_ASM1448957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe7e1ffa-55c7-496d-8724-eeeef08b0847/dqc_reference/reference_markers_gtdb.fasta -out GCF_014489575.1_ASM1448957v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:10,485] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:10,494] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:10,494] [INFO] Target genome list was writen to GCF_014489575.1_ASM1448957v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:10,503] [INFO] Task started: fastANI
[2024-01-24 12:31:10,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgecae6efb-0b7a-4b95-a43c-478f29edb5de/GCF_014489575.1_ASM1448957v1_genomic.fna.gz --refList GCF_014489575.1_ASM1448957v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014489575.1_ASM1448957v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:18,419] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:18,426] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:18,426] [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_014489575.1	s__Arachnia defluvii	100.0	1288	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011174705.1	s__Arachnia coleopterorum	81.7571	675	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998865.1	s__Arachnia flavescens	81.7546	611	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001997345.1	s__Arachnia aquimaris	81.387	658	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693815.1	s__Arachnia lapidicapta	81.2256	552	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.86	97.76	0.95	0.93	4	-
GCA_016714275.1	s__Arachnia sp016714275	80.7293	534	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001997295.1	s__Arachnia flava	80.534	484	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	99.99	99.99	1.00	1.00	2	-
GCA_012837465.1	s__Arachnia sp012837465	80.2964	411	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826065.2	s__Arachnia massiliensis	80.2265	510	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017815535.1	s__Arachnia sp001956895	79.9362	517	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.64	95.92	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:18,428] [INFO] GTDB search result was written to GCF_014489575.1_ASM1448957v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:18,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:18,432] [INFO] DFAST_QC result json was written to GCF_014489575.1_ASM1448957v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:18,432] [INFO] DFAST_QC completed!
[2024-01-24 12:31:18,432] [INFO] Total running time: 0h1m13s