[2024-01-24 11:22:49,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e7a77a3-3ef0-4283-a2f1-1d5f065922fb/dqc_reference
[2024-01-24 11:22:50,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,709] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,709] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4f43bb2-ded4-4517-8d99-2d9a651c784e/GCF_019973735.1_ASM1997373v1_genomic.fna.gz | prodigal -d GCF_019973735.1_ASM1997373v1_genomic.fna/cds.fna -a GCF_019973735.1_ASM1997373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:00,765] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:00,766] [INFO] Task started: HMMsearch
[2024-01-24 11:23:00,766] [INFO] Running command: hmmsearch --tblout GCF_019973735.1_ASM1997373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e7a77a3-3ef0-4283-a2f1-1d5f065922fb/dqc_reference/reference_markers.hmm GCF_019973735.1_ASM1997373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:01,013] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:01,015] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb4f43bb2-ded4-4517-8d99-2d9a651c784e/GCF_019973735.1_ASM1997373v1_genomic.fna.gz]
[2024-01-24 11:23:01,043] [INFO] Query marker FASTA was written to GCF_019973735.1_ASM1997373v1_genomic.fna/markers.fasta
[2024-01-24 11:23:01,043] [INFO] Task started: Blastn
[2024-01-24 11:23:01,043] [INFO] Running command: blastn -query GCF_019973735.1_ASM1997373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e7a77a3-3ef0-4283-a2f1-1d5f065922fb/dqc_reference/reference_markers.fasta -out GCF_019973735.1_ASM1997373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:01,668] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:01,671] [INFO] Selected 14 target genomes.
[2024-01-24 11:23:01,671] [INFO] Target genome list was writen to GCF_019973735.1_ASM1997373v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:01,675] [INFO] Task started: fastANI
[2024-01-24 11:23:01,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f43bb2-ded4-4517-8d99-2d9a651c784e/GCF_019973735.1_ASM1997373v1_genomic.fna.gz --refList GCF_019973735.1_ASM1997373v1_genomic.fna/target_genomes.txt --output GCF_019973735.1_ASM1997373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:10,449] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:10,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e7a77a3-3ef0-4283-a2f1-1d5f065922fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:10,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e7a77a3-3ef0-4283-a2f1-1d5f065922fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:10,466] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:23:10,466] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:10,466] [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
Arachnia rubra	strain=SK-1	GCA_019973735.1	1547448	1547448	type	True	100.0	1105	1105	95	conclusive
Arachnia propionica	strain=NCTC12967	GCA_900637725.1	1750	1750	type	True	82.8738	667	1105	95	below_threshold
Arachnia propionica	strain=NBRC 14587	GCA_001592325.1	1750	1750	type	True	82.7975	659	1105	95	below_threshold
[Pseudopropionibacterium] massiliense	strain=Marseille-P6184	GCA_900607225.1	2220000	2220000	type	True	82.5829	651	1105	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	78.0201	220	1105	95	below_threshold
Tessaracoccus rhinocerotis	strain=YIM 101269	GCA_007197885.1	1689449	1689449	type	True	77.9771	235	1105	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	77.8244	219	1105	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	77.2948	150	1105	95	below_threshold
Naumannella halotolerans	strain=DSM 24323	GCA_004364645.1	993414	993414	type	True	77.0201	83	1105	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	76.7993	108	1105	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	76.4081	101	1105	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	76.0676	78	1105	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.0506	66	1105	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	75.9033	69	1105	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:10,468] [INFO] DFAST Taxonomy check result was written to GCF_019973735.1_ASM1997373v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:10,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:10,469] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:10,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e7a77a3-3ef0-4283-a2f1-1d5f065922fb/dqc_reference/checkm_data
[2024-01-24 11:23:10,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:10,502] [INFO] Task started: CheckM
[2024-01-24 11:23:10,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019973735.1_ASM1997373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019973735.1_ASM1997373v1_genomic.fna/checkm_input GCF_019973735.1_ASM1997373v1_genomic.fna/checkm_result
[2024-01-24 11:23:44,281] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:44,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:44,303] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:44,303] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:44,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019973735.1_ASM1997373v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:44,304] [INFO] Task started: Blastn
[2024-01-24 11:23:44,304] [INFO] Running command: blastn -query GCF_019973735.1_ASM1997373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e7a77a3-3ef0-4283-a2f1-1d5f065922fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_019973735.1_ASM1997373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:45,165] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:45,170] [INFO] Selected 10 target genomes.
[2024-01-24 11:23:45,170] [INFO] Target genome list was writen to GCF_019973735.1_ASM1997373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:45,177] [INFO] Task started: fastANI
[2024-01-24 11:23:45,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f43bb2-ded4-4517-8d99-2d9a651c784e/GCF_019973735.1_ASM1997373v1_genomic.fna.gz --refList GCF_019973735.1_ASM1997373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019973735.1_ASM1997373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:52,042] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:52,055] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:52,055] [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_018128325.1	s__Arachnia rubra	99.9986	1103	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	99.26	99.21	0.97	0.97	4	conclusive
GCF_900637725.1	s__Arachnia propionica	82.8405	665	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.87	97.26	0.96	0.91	9	-
GCF_900607225.1	s__Arachnia sp900607225	82.575	652	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372155.1	s__Arachnia sp905372155	82.4809	594	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013333945.2	s__Arachnia sp013333945	80.8973	505	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003859805.1	s__Arachnia propionica_C	79.2856	375	1105	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	78.0047	221	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197885.1	s__Arachnia rhinocerotis	77.9771	235	1105	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	77.7332	223	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514785.1	s__Arachnia sp012514785	77.2137	106	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:52,057] [INFO] GTDB search result was written to GCF_019973735.1_ASM1997373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:52,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:52,061] [INFO] DFAST_QC result json was written to GCF_019973735.1_ASM1997373v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:52,061] [INFO] DFAST_QC completed!
[2024-01-24 11:23:52,061] [INFO] Total running time: 0h1m3s