[2024-01-24 12:31:19,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:19,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:19,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fa5f6da-61d4-4ea2-b186-0fb120c5a690/dqc_reference
[2024-01-24 12:31:21,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:21,095] [INFO] Task started: Prodigal
[2024-01-24 12:31:21,095] [INFO] Running command: gunzip -c /var/lib/cwl/stg120909f6-5418-451a-87bd-b076fbb82b8d/GCF_001997345.1_ASM199734v1_genomic.fna.gz | prodigal -d GCF_001997345.1_ASM199734v1_genomic.fna/cds.fna -a GCF_001997345.1_ASM199734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:32,835] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:32,835] [INFO] Task started: HMMsearch
[2024-01-24 12:31:32,835] [INFO] Running command: hmmsearch --tblout GCF_001997345.1_ASM199734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fa5f6da-61d4-4ea2-b186-0fb120c5a690/dqc_reference/reference_markers.hmm GCF_001997345.1_ASM199734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:33,065] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:33,067] [INFO] Found 6/6 markers.
[2024-01-24 12:31:33,104] [INFO] Query marker FASTA was written to GCF_001997345.1_ASM199734v1_genomic.fna/markers.fasta
[2024-01-24 12:31:33,105] [INFO] Task started: Blastn
[2024-01-24 12:31:33,105] [INFO] Running command: blastn -query GCF_001997345.1_ASM199734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fa5f6da-61d4-4ea2-b186-0fb120c5a690/dqc_reference/reference_markers.fasta -out GCF_001997345.1_ASM199734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:34,166] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:34,169] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:34,170] [INFO] Target genome list was writen to GCF_001997345.1_ASM199734v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:34,173] [INFO] Task started: fastANI
[2024-01-24 12:31:34,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg120909f6-5418-451a-87bd-b076fbb82b8d/GCF_001997345.1_ASM199734v1_genomic.fna.gz --refList GCF_001997345.1_ASM199734v1_genomic.fna/target_genomes.txt --output GCF_001997345.1_ASM199734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:42,820] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:42,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fa5f6da-61d4-4ea2-b186-0fb120c5a690/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:42,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fa5f6da-61d4-4ea2-b186-0fb120c5a690/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:42,830] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:42,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:42,830] [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 aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	100.0	1311	1311	95	conclusive
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	82.8224	764	1311	95	below_threshold
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	82.6557	761	1311	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	81.4128	652	1311	95	below_threshold
Tessaracoccus bendigoensis	strain=DSM 12906	GCA_900141915.1	72764	72764	type	True	81.3702	613	1311	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	80.5243	508	1311	95	below_threshold
Tessaracoccus flavus	strain=RP1	GCA_001997295.1	1610493	1610493	type	True	80.016	467	1311	95	below_threshold
Tessaracoccus flavus	strain=RP1	GCA_900107385.1	1610493	1610493	type	True	79.917	470	1311	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	78.9143	405	1311	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	78.2785	328	1311	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	76.9364	275	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:42,832] [INFO] DFAST Taxonomy check result was written to GCF_001997345.1_ASM199734v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:42,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:42,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:42,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fa5f6da-61d4-4ea2-b186-0fb120c5a690/dqc_reference/checkm_data
[2024-01-24 12:31:42,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:42,871] [INFO] Task started: CheckM
[2024-01-24 12:31:42,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001997345.1_ASM199734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001997345.1_ASM199734v1_genomic.fna/checkm_input GCF_001997345.1_ASM199734v1_genomic.fna/checkm_result
[2024-01-24 12:32:21,430] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:21,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:21,454] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:21,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:21,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001997345.1_ASM199734v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:21,455] [INFO] Task started: Blastn
[2024-01-24 12:32:21,455] [INFO] Running command: blastn -query GCF_001997345.1_ASM199734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fa5f6da-61d4-4ea2-b186-0fb120c5a690/dqc_reference/reference_markers_gtdb.fasta -out GCF_001997345.1_ASM199734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:23,128] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:23,131] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:23,131] [INFO] Target genome list was writen to GCF_001997345.1_ASM199734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:23,143] [INFO] Task started: fastANI
[2024-01-24 12:32:23,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg120909f6-5418-451a-87bd-b076fbb82b8d/GCF_001997345.1_ASM199734v1_genomic.fna.gz --refList GCF_001997345.1_ASM199734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001997345.1_ASM199734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:30,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:30,978] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:30,978] [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_001997345.1	s__Arachnia aquimaris	100.0	1311	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001998865.1	s__Arachnia flavescens	82.8224	764	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011174705.1	s__Arachnia coleopterorum	82.6307	763	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489575.1	s__Arachnia defluvii	81.4234	651	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141915.1	s__Arachnia bendigoensis	81.3838	612	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714275.1	s__Arachnia sp016714275	80.7186	587	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837465.1	s__Arachnia sp012837465	80.6914	423	1311	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	80.4203	517	1311	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	80.0509	532	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.64	95.92	0.92	0.88	4	-
GCF_001997295.1	s__Arachnia flava	80.0206	467	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:30,979] [INFO] GTDB search result was written to GCF_001997345.1_ASM199734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:30,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:30,984] [INFO] DFAST_QC result json was written to GCF_001997345.1_ASM199734v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:30,984] [INFO] DFAST_QC completed!
[2024-01-24 12:32:30,984] [INFO] Total running time: 0h1m11s