[2024-01-24 14:46:35,375] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg2708f11d-837a-4662-ab22-b320ea54dcec/dqc_reference
[2024-01-24 14:46:36,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,661] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,662] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c1db6e7-3b59-458d-8e06-3a22bddab181/GCF_011758645.1_ASM1175864v1_genomic.fna.gz | prodigal -d GCF_011758645.1_ASM1175864v1_genomic.fna/cds.fna -a GCF_011758645.1_ASM1175864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:48,521] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:48,522] [INFO] Task started: HMMsearch
[2024-01-24 14:46:48,522] [INFO] Running command: hmmsearch --tblout GCF_011758645.1_ASM1175864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2708f11d-837a-4662-ab22-b320ea54dcec/dqc_reference/reference_markers.hmm GCF_011758645.1_ASM1175864v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:48,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:48,814] [INFO] Found 6/6 markers.
[2024-01-24 14:46:48,861] [INFO] Query marker FASTA was written to GCF_011758645.1_ASM1175864v1_genomic.fna/markers.fasta
[2024-01-24 14:46:48,861] [INFO] Task started: Blastn
[2024-01-24 14:46:48,861] [INFO] Running command: blastn -query GCF_011758645.1_ASM1175864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2708f11d-837a-4662-ab22-b320ea54dcec/dqc_reference/reference_markers.fasta -out GCF_011758645.1_ASM1175864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:49,943] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:49,948] [INFO] Selected 25 target genomes.
[2024-01-24 14:46:49,948] [INFO] Target genome list was writen to GCF_011758645.1_ASM1175864v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:49,960] [INFO] Task started: fastANI
[2024-01-24 14:46:49,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c1db6e7-3b59-458d-8e06-3a22bddab181/GCF_011758645.1_ASM1175864v1_genomic.fna.gz --refList GCF_011758645.1_ASM1175864v1_genomic.fna/target_genomes.txt --output GCF_011758645.1_ASM1175864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:07,807] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:07,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2708f11d-837a-4662-ab22-b320ea54dcec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:07,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2708f11d-837a-4662-ab22-b320ea54dcec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:07,826] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:07,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:07,827] [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
Brooklawnia cerclae	strain=DSM 19609	GCA_011758645.1	349934	349934	type	True	100.0	1258	1260	95	conclusive
Propionibacterium acidifaciens	strain=DSM 21887	GCA_000426605.1	556499	556499	type	True	77.9613	252	1260	95	below_threshold
Propionibacterium australiense	strain=NCTC13651	GCA_900637915.1	119981	119981	type	True	77.78	248	1260	95	below_threshold
Propionibacterium australiense	strain=NML98A072	GCA_003666605.1	119981	119981	type	True	77.7777	240	1260	95	below_threshold
Propionibacterium cyclohexanicum	strain=DSM 16859	GCA_900111365.1	64702	64702	type	True	77.719	198	1260	95	below_threshold
Acidipropionibacterium virtanenii	strain=JS278	GCA_003325455.1	2057246	2057246	type	True	77.6995	186	1260	95	below_threshold
Acidipropionibacterium acidipropionici	strain=CGMCC 1.2230	GCA_001441165.1	1748	1748	type	True	77.537	197	1260	95	below_threshold
Aestuariimicrobium kwangyangense	strain=DSM 21549	GCA_000421525.1	396389	396389	type	True	77.3526	191	1260	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.3421	243	1260	95	below_threshold
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	77.3112	195	1260	95	below_threshold
Acidipropionibacterium acidipropionici	strain=DSM 4900	GCA_000427845.1	1748	1748	type	True	77.2709	200	1260	95	below_threshold
Raineyella fluvialis	strain=CBA3103	GCA_009646095.1	2662261	2662261	type	True	77.1571	173	1260	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	76.9992	248	1260	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	76.9969	238	1260	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	76.9849	197	1260	95	below_threshold
[Pseudopropionibacterium] massiliense	strain=Marseille-P6184	GCA_900607225.1	2220000	2220000	type	True	76.9511	146	1260	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	76.7191	200	1260	95	below_threshold
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	76.6717	201	1260	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	76.439	167	1260	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	76.4067	213	1260	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	75.7551	189	1260	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.2458	100	1260	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	74.9605	67	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:07,829] [INFO] DFAST Taxonomy check result was written to GCF_011758645.1_ASM1175864v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:07,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:07,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:07,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2708f11d-837a-4662-ab22-b320ea54dcec/dqc_reference/checkm_data
[2024-01-24 14:47:07,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:07,871] [INFO] Task started: CheckM
[2024-01-24 14:47:07,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011758645.1_ASM1175864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011758645.1_ASM1175864v1_genomic.fna/checkm_input GCF_011758645.1_ASM1175864v1_genomic.fna/checkm_result
[2024-01-24 14:47:54,585] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:54,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:54,605] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:54,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:54,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011758645.1_ASM1175864v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:54,607] [INFO] Task started: Blastn
[2024-01-24 14:47:54,607] [INFO] Running command: blastn -query GCF_011758645.1_ASM1175864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2708f11d-837a-4662-ab22-b320ea54dcec/dqc_reference/reference_markers_gtdb.fasta -out GCF_011758645.1_ASM1175864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:56,232] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:56,235] [INFO] Selected 20 target genomes.
[2024-01-24 14:47:56,236] [INFO] Target genome list was writen to GCF_011758645.1_ASM1175864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:56,258] [INFO] Task started: fastANI
[2024-01-24 14:47:56,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c1db6e7-3b59-458d-8e06-3a22bddab181/GCF_011758645.1_ASM1175864v1_genomic.fna.gz --refList GCF_011758645.1_ASM1175864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011758645.1_ASM1175864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:10,436] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:10,458] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:10,459] [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_011758645.1	s__Brooklawnia cerclae	100.0	1256	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brooklawnia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012517405.1	s__Brooklawnia sp012517405	78.6298	358	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brooklawnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426605.1	s__Propionibacterium acidifaciens	77.9471	253	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.24	99.02	0.93	0.90	4	-
GCA_012517115.1	s__Brooklawnia sp012517115	77.7787	228	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brooklawnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666605.1	s__Propionibacterium australiense	77.7461	240	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.91	99.75	0.98	0.97	4	-
GCF_900289195.1	s__Propionibacterium sp900289195	77.6639	230	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.03	99.03	0.94	0.94	2	-
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	77.5214	198	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
GCF_011393335.1	s__Brevilactibacter coleopterorum	77.3741	245	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826085.1	s__Nigerium massiliense	77.3422	232	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Nigerium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017306015.1	s__Propionicimonas sp017306015	77.1966	230	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352975.1	s__Aestuariimicrobium ganziense	76.9991	248	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900607225.1	s__Arachnia sp900607225	76.9511	146	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	76.7077	201	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002250625.1	s__Enemella sp002250625	76.6609	202	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.13	98.13	0.89	0.89	2	-
GCA_018055925.1	s__Micropruina sp018055925	76.5996	207	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	76.5011	237	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765225.1	s__Leifsonia sp009765225	76.1335	106	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	75.719	171	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:10,460] [INFO] GTDB search result was written to GCF_011758645.1_ASM1175864v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:10,461] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:10,466] [INFO] DFAST_QC result json was written to GCF_011758645.1_ASM1175864v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:10,467] [INFO] DFAST_QC completed!
[2024-01-24 14:48:10,467] [INFO] Total running time: 0h1m35s