[2024-01-24 11:27:04,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg4602497b-0c4d-4d54-aca6-bbac716835de/dqc_reference
[2024-01-24 11:27:05,975] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,976] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,976] [INFO] Running command: gunzip -c /var/lib/cwl/stg26c499a9-6f22-4849-983f-2f39f08929cf/GCF_900607225.1_PRJEB27265_genomic.fna.gz | prodigal -d GCF_900607225.1_PRJEB27265_genomic.fna/cds.fna -a GCF_900607225.1_PRJEB27265_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:16,842] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:16,842] [INFO] Task started: HMMsearch
[2024-01-24 11:27:16,842] [INFO] Running command: hmmsearch --tblout GCF_900607225.1_PRJEB27265_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4602497b-0c4d-4d54-aca6-bbac716835de/dqc_reference/reference_markers.hmm GCF_900607225.1_PRJEB27265_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:17,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:17,112] [INFO] Found 6/6 markers.
[2024-01-24 11:27:17,143] [INFO] Query marker FASTA was written to GCF_900607225.1_PRJEB27265_genomic.fna/markers.fasta
[2024-01-24 11:27:17,144] [INFO] Task started: Blastn
[2024-01-24 11:27:17,144] [INFO] Running command: blastn -query GCF_900607225.1_PRJEB27265_genomic.fna/markers.fasta -db /var/lib/cwl/stg4602497b-0c4d-4d54-aca6-bbac716835de/dqc_reference/reference_markers.fasta -out GCF_900607225.1_PRJEB27265_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:17,987] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:17,990] [INFO] Selected 12 target genomes.
[2024-01-24 11:27:17,990] [INFO] Target genome list was writen to GCF_900607225.1_PRJEB27265_genomic.fna/target_genomes.txt
[2024-01-24 11:27:17,997] [INFO] Task started: fastANI
[2024-01-24 11:27:17,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c499a9-6f22-4849-983f-2f39f08929cf/GCF_900607225.1_PRJEB27265_genomic.fna.gz --refList GCF_900607225.1_PRJEB27265_genomic.fna/target_genomes.txt --output GCF_900607225.1_PRJEB27265_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:26,674] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:26,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4602497b-0c4d-4d54-aca6-bbac716835de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:26,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4602497b-0c4d-4d54-aca6-bbac716835de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:26,691] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:26,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:26,691] [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
[Pseudopropionibacterium] massiliense	strain=Marseille-P6184	GCA_900607225.1	2220000	2220000	type	True	100.0	1156	1156	95	conclusive
Arachnia propionica	strain=NCTC12967	GCA_900637725.1	1750	1750	type	True	91.054	905	1156	95	below_threshold
Arachnia propionica	strain=NBRC 14587	GCA_001592325.1	1750	1750	type	True	90.98	911	1156	95	below_threshold
Arachnia rubra	strain=SK-1	GCA_019973735.1	1547448	1547448	type	True	82.5068	647	1156	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	78.4306	258	1156	95	below_threshold
Tessaracoccus antarcticus	strain=JDX10	GCA_003688855.1	2479848	2479848	type	True	78.3286	242	1156	95	below_threshold
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	78.2198	274	1156	95	below_threshold
Tessaracoccus rhinocerotis	strain=YIM 101269	GCA_007197885.1	1689449	1689449	type	True	78.1736	309	1156	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	78.0215	279	1156	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	77.628	193	1156	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	76.6275	132	1156	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	76.351	131	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:26,693] [INFO] DFAST Taxonomy check result was written to GCF_900607225.1_PRJEB27265_genomic.fna/tc_result.tsv
[2024-01-24 11:27:26,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:26,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:26,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4602497b-0c4d-4d54-aca6-bbac716835de/dqc_reference/checkm_data
[2024-01-24 11:27:26,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:26,729] [INFO] Task started: CheckM
[2024-01-24 11:27:26,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900607225.1_PRJEB27265_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900607225.1_PRJEB27265_genomic.fna/checkm_input GCF_900607225.1_PRJEB27265_genomic.fna/checkm_result
[2024-01-24 11:28:11,762] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:11,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:11,787] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:11,787] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:11,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900607225.1_PRJEB27265_genomic.fna/markers.fasta)
[2024-01-24 11:28:11,788] [INFO] Task started: Blastn
[2024-01-24 11:28:11,789] [INFO] Running command: blastn -query GCF_900607225.1_PRJEB27265_genomic.fna/markers.fasta -db /var/lib/cwl/stg4602497b-0c4d-4d54-aca6-bbac716835de/dqc_reference/reference_markers_gtdb.fasta -out GCF_900607225.1_PRJEB27265_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:12,968] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:12,972] [INFO] Selected 7 target genomes.
[2024-01-24 11:28:12,972] [INFO] Target genome list was writen to GCF_900607225.1_PRJEB27265_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:12,982] [INFO] Task started: fastANI
[2024-01-24 11:28:12,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c499a9-6f22-4849-983f-2f39f08929cf/GCF_900607225.1_PRJEB27265_genomic.fna.gz --refList GCF_900607225.1_PRJEB27265_genomic.fna/target_genomes_gtdb.txt --output GCF_900607225.1_PRJEB27265_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:19,267] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:19,281] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:19,282] [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_900607225.1	s__Arachnia sp900607225	100.0	1156	1156	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_905372155.1	s__Arachnia sp905372155	91.51	855	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637725.1	s__Arachnia propionica	91.054	905	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.87	97.26	0.96	0.91	9	-
GCA_013333945.2	s__Arachnia sp013333945	87.8476	762	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018128325.1	s__Arachnia rubra	82.5777	639	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	99.26	99.21	0.97	0.97	4	-
GCF_003932785.1	s__Arachnia propionica_B	79.639	441	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014164775.1	s__Arachnia sp014164775	78.3465	262	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.46	97.46	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:19,284] [INFO] GTDB search result was written to GCF_900607225.1_PRJEB27265_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:19,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:19,289] [INFO] DFAST_QC result json was written to GCF_900607225.1_PRJEB27265_genomic.fna/dqc_result.json
[2024-01-24 11:28:19,290] [INFO] DFAST_QC completed!
[2024-01-24 11:28:19,290] [INFO] Total running time: 0h1m15s