[2024-01-24 12:45:20,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg463f32f7-cd2a-46f7-98a8-ae7ecd5d7cc5/dqc_reference
[2024-01-24 12:45:21,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:21,640] [INFO] Task started: Prodigal
[2024-01-24 12:45:21,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgf94022f5-c83d-49ab-ad43-49e3ac42afe1/GCF_015352975.1_ASM1535297v1_genomic.fna.gz | prodigal -d GCF_015352975.1_ASM1535297v1_genomic.fna/cds.fna -a GCF_015352975.1_ASM1535297v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:31,613] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:31,613] [INFO] Task started: HMMsearch
[2024-01-24 12:45:31,613] [INFO] Running command: hmmsearch --tblout GCF_015352975.1_ASM1535297v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg463f32f7-cd2a-46f7-98a8-ae7ecd5d7cc5/dqc_reference/reference_markers.hmm GCF_015352975.1_ASM1535297v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:31,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:31,857] [INFO] Found 6/6 markers.
[2024-01-24 12:45:31,886] [INFO] Query marker FASTA was written to GCF_015352975.1_ASM1535297v1_genomic.fna/markers.fasta
[2024-01-24 12:45:31,886] [INFO] Task started: Blastn
[2024-01-24 12:45:31,886] [INFO] Running command: blastn -query GCF_015352975.1_ASM1535297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463f32f7-cd2a-46f7-98a8-ae7ecd5d7cc5/dqc_reference/reference_markers.fasta -out GCF_015352975.1_ASM1535297v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:33,040] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:33,043] [INFO] Selected 23 target genomes.
[2024-01-24 12:45:33,043] [INFO] Target genome list was writen to GCF_015352975.1_ASM1535297v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:33,063] [INFO] Task started: fastANI
[2024-01-24 12:45:33,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgf94022f5-c83d-49ab-ad43-49e3ac42afe1/GCF_015352975.1_ASM1535297v1_genomic.fna.gz --refList GCF_015352975.1_ASM1535297v1_genomic.fna/target_genomes.txt --output GCF_015352975.1_ASM1535297v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:48,829] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:48,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg463f32f7-cd2a-46f7-98a8-ae7ecd5d7cc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:48,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg463f32f7-cd2a-46f7-98a8-ae7ecd5d7cc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:48,853] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:48,853] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:48,853] [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
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	100.0	1033	1034	95	conclusive
Aestuariimicrobium kwangyangense	strain=DSM 21549	GCA_000421525.1	396389	396389	type	True	79.7596	468	1034	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	79.1793	342	1034	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	78.7436	348	1034	95	below_threshold
Luteococcus japonicus	strain=DSM 10546	GCA_003752415.1	33984	33984	type	True	78.6774	354	1034	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	78.6298	314	1034	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	78.5744	302	1034	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.4743	349	1034	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	78.4696	390	1034	95	below_threshold
Tessaracoccus rhinocerotis	strain=YIM 101269	GCA_007197885.1	1689449	1689449	type	True	78.462	276	1034	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	78.4291	378	1034	95	below_threshold
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	78.3861	269	1034	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	78.317	371	1034	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_900182665.1	433330	433330	type	True	77.9279	238	1034	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_004324765.1	433330	433330	type	True	77.8741	239	1034	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.7504	279	1034	95	below_threshold
Naumannella halotolerans	strain=DSM 24323	GCA_004364645.1	993414	993414	type	True	77.7159	224	1034	95	below_threshold
Propionibacterium freudenreichii subsp. freudenreichii	strain=DSM 20271	GCA_000940845.1	66712	1744	type	True	77.7133	193	1034	95	below_threshold
Propionibacterium australiense	strain=NML98A072	GCA_003666605.1	119981	119981	type	True	77.706	218	1034	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	77.6347	265	1034	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	77.5224	273	1034	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.1262	241	1034	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	76.6835	254	1034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:48,855] [INFO] DFAST Taxonomy check result was written to GCF_015352975.1_ASM1535297v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:48,856] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:48,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:48,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg463f32f7-cd2a-46f7-98a8-ae7ecd5d7cc5/dqc_reference/checkm_data
[2024-01-24 12:45:48,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:48,893] [INFO] Task started: CheckM
[2024-01-24 12:45:48,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015352975.1_ASM1535297v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015352975.1_ASM1535297v1_genomic.fna/checkm_input GCF_015352975.1_ASM1535297v1_genomic.fna/checkm_result
[2024-01-24 12:46:48,708] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:48,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:48,731] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:48,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:48,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015352975.1_ASM1535297v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:48,732] [INFO] Task started: Blastn
[2024-01-24 12:46:48,732] [INFO] Running command: blastn -query GCF_015352975.1_ASM1535297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463f32f7-cd2a-46f7-98a8-ae7ecd5d7cc5/dqc_reference/reference_markers_gtdb.fasta -out GCF_015352975.1_ASM1535297v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:50,521] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:50,526] [INFO] Selected 23 target genomes.
[2024-01-24 12:46:50,526] [INFO] Target genome list was writen to GCF_015352975.1_ASM1535297v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:50,587] [INFO] Task started: fastANI
[2024-01-24 12:46:50,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgf94022f5-c83d-49ab-ad43-49e3ac42afe1/GCF_015352975.1_ASM1535297v1_genomic.fna.gz --refList GCF_015352975.1_ASM1535297v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015352975.1_ASM1535297v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:05,471] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:05,494] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:05,494] [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_015352975.1	s__Aestuariimicrobium ganziense	100.0	1033	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000421525.1	s__Aestuariimicrobium kwangyangense	79.7199	472	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355265.1	s__Aestuariimicrobium sp017355265	79.3647	379	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569205.1	s__Brevilactibacter sp014164685	79.128	371	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	99.00	98.00	0.92	0.83	3	-
GCA_012838755.1	s__Brevilactibacter sp012838755	78.9387	299	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387005.1	s__Luteococcus avicola	78.7718	285	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Luteococcus	95.0	96.77	96.77	0.82	0.82	2	-
GCF_011393335.1	s__Brevilactibacter coleopterorum	78.7147	351	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998865.1	s__Arachnia flavescens	78.588	301	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	78.4568	351	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_009742705.1	s__Auraticoccus cholistanensis	78.4399	377	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711205.1	s__Micropruina sp016711205	78.4077	321	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563675.1	s__Propionicimonas paludicola	78.3737	271	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101785.1	s__Auraticoccus monumenti	78.3076	373	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	78.1355	288	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900289045.1	s__Micropruina glycogenica	78.049	347	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306015.1	s__Propionicimonas sp017306015	78.0352	329	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843035.1	s__Propionicimonas sp002843035	78.0169	291	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	77.969	354	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182665.1	s__Propioniciclava tarda	77.9174	240	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009557055.1	s__Nocardioides sp009557055	77.7397	270	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000940845.1	s__Propionibacterium freudenreichii	77.7133	193	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	98.89	98.71	0.93	0.90	43	-
GCF_014127485.1	s__Nocardioides sp014127485	77.4789	277	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_000620705.1	s__Nocardioides sp000620705	77.3251	269	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:05,496] [INFO] GTDB search result was written to GCF_015352975.1_ASM1535297v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:05,496] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:05,501] [INFO] DFAST_QC result json was written to GCF_015352975.1_ASM1535297v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:05,501] [INFO] DFAST_QC completed!
[2024-01-24 12:47:05,501] [INFO] Total running time: 0h1m45s