[2024-01-24 13:09:49,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg1336ba88-8924-4135-bc60-605d1cc1be5f/dqc_reference
[2024-01-24 13:09:50,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,532] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,532] [INFO] Running command: gunzip -c /var/lib/cwl/stgdefc6170-c72f-459b-b4fb-33cace991005/GCF_019710575.1_ASM1971057v1_genomic.fna.gz | prodigal -d GCF_019710575.1_ASM1971057v1_genomic.fna/cds.fna -a GCF_019710575.1_ASM1971057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:28,910] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:28,911] [INFO] Task started: HMMsearch
[2024-01-24 13:10:28,911] [INFO] Running command: hmmsearch --tblout GCF_019710575.1_ASM1971057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1336ba88-8924-4135-bc60-605d1cc1be5f/dqc_reference/reference_markers.hmm GCF_019710575.1_ASM1971057v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:29,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:29,329] [INFO] Found 6/6 markers.
[2024-01-24 13:10:29,406] [INFO] Query marker FASTA was written to GCF_019710575.1_ASM1971057v1_genomic.fna/markers.fasta
[2024-01-24 13:10:29,407] [INFO] Task started: Blastn
[2024-01-24 13:10:29,407] [INFO] Running command: blastn -query GCF_019710575.1_ASM1971057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1336ba88-8924-4135-bc60-605d1cc1be5f/dqc_reference/reference_markers.fasta -out GCF_019710575.1_ASM1971057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:30,692] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:30,696] [INFO] Selected 18 target genomes.
[2024-01-24 13:10:30,697] [INFO] Target genome list was writen to GCF_019710575.1_ASM1971057v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:30,748] [INFO] Task started: fastANI
[2024-01-24 13:10:30,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgdefc6170-c72f-459b-b4fb-33cace991005/GCF_019710575.1_ASM1971057v1_genomic.fna.gz --refList GCF_019710575.1_ASM1971057v1_genomic.fna/target_genomes.txt --output GCF_019710575.1_ASM1971057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:11:03,384] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:03,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1336ba88-8924-4135-bc60-605d1cc1be5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:11:03,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1336ba88-8924-4135-bc60-605d1cc1be5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:11:03,404] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:11:03,405] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:11:03,405] [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
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	85.4286	2263	3501	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	85.3101	2241	3501	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	85.1653	2217	3501	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	84.8946	2098	3501	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	84.8931	2167	3501	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	84.8886	2124	3501	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	83.2634	2060	3501	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	83.2068	2006	3501	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.363	1526	3501	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.8158	825	3501	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.5885	1085	3501	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	78.4173	973	3501	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	76.4429	485	3501	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	76.266	562	3501	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.2244	671	3501	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	76.0883	253	3501	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	75.9479	256	3501	95	below_threshold
Nakamurella aerolata	strain=DB0629	GCA_013002705.1	1656892	1656892	type	True	75.8907	394	3501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:11:03,407] [INFO] DFAST Taxonomy check result was written to GCF_019710575.1_ASM1971057v1_genomic.fna/tc_result.tsv
[2024-01-24 13:11:03,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:11:03,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:11:03,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1336ba88-8924-4135-bc60-605d1cc1be5f/dqc_reference/checkm_data
[2024-01-24 13:11:03,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:11:03,504] [INFO] Task started: CheckM
[2024-01-24 13:11:03,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019710575.1_ASM1971057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019710575.1_ASM1971057v1_genomic.fna/checkm_input GCF_019710575.1_ASM1971057v1_genomic.fna/checkm_result
[2024-01-24 13:12:57,995] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:57,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:58,023] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:58,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:58,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019710575.1_ASM1971057v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:58,024] [INFO] Task started: Blastn
[2024-01-24 13:12:58,024] [INFO] Running command: blastn -query GCF_019710575.1_ASM1971057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1336ba88-8924-4135-bc60-605d1cc1be5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019710575.1_ASM1971057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:59,881] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:59,886] [INFO] Selected 15 target genomes.
[2024-01-24 13:12:59,886] [INFO] Target genome list was writen to GCF_019710575.1_ASM1971057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:01,145] [INFO] Task started: fastANI
[2024-01-24 13:13:01,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgdefc6170-c72f-459b-b4fb-33cace991005/GCF_019710575.1_ASM1971057v1_genomic.fna.gz --refList GCF_019710575.1_ASM1971057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019710575.1_ASM1971057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:33,248] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:33,263] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:13:33,264] [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_016785085.1	s__Actinoplanes sp016785085	85.4033	2269	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016834655.1	s__Actinoplanes sp016834655	85.2977	2241	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	85.1706	2216	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003999975.1	s__Actinoplanes sp003999975	84.9754	2137	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018829635.1	s__Actinoplanes bogorensis	84.9193	2162	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362215.1	s__Actinoplanes brasiliensis	84.9107	2119	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	83.2682	2059	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	83.198	2008	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332695.1	s__Actinoplanes toevensis	82.0532	1850	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862375.1	s__Actinoplanes rishiriensis	81.7589	1762	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720335.1	s__Marmoricola aequoreus	76.4418	488	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653215.1	s__Pseudolysinimonas yzui	76.2972	250	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125335.1	s__WLRQ01 sp016125335	76.2107	465	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	76.1045	704	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335115.1	s__Quadrisphaera sp006335115	76.0417	531	3501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:33,265] [INFO] GTDB search result was written to GCF_019710575.1_ASM1971057v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:33,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:33,270] [INFO] DFAST_QC result json was written to GCF_019710575.1_ASM1971057v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:33,270] [INFO] DFAST_QC completed!
[2024-01-24 13:13:33,270] [INFO] Total running time: 0h3m44s