[2023-06-28 11:04:03,315] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:04:03,317] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:04:03,317] [INFO] DQC Reference Directory: /var/lib/cwl/stga569e220-2503-4c17-9442-aaca99e144db/dqc_reference
[2023-06-28 11:04:05,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:04:05,409] [INFO] Task started: Prodigal
[2023-06-28 11:04:05,409] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf34dd55-8992-4d33-9132-d8c5c5cb7a3a/GCA_005885115.1_ASM588511v1_genomic.fna.gz | prodigal -d GCA_005885115.1_ASM588511v1_genomic.fna/cds.fna -a GCA_005885115.1_ASM588511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:04:13,235] [INFO] Task succeeded: Prodigal
[2023-06-28 11:04:13,236] [INFO] Task started: HMMsearch
[2023-06-28 11:04:13,236] [INFO] Running command: hmmsearch --tblout GCA_005885115.1_ASM588511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga569e220-2503-4c17-9442-aaca99e144db/dqc_reference/reference_markers.hmm GCA_005885115.1_ASM588511v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:04:13,459] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:04:13,460] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcf34dd55-8992-4d33-9132-d8c5c5cb7a3a/GCA_005885115.1_ASM588511v1_genomic.fna.gz]
[2023-06-28 11:04:13,515] [INFO] Query marker FASTA was written to GCA_005885115.1_ASM588511v1_genomic.fna/markers.fasta
[2023-06-28 11:04:13,516] [INFO] Task started: Blastn
[2023-06-28 11:04:13,516] [INFO] Running command: blastn -query GCA_005885115.1_ASM588511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga569e220-2503-4c17-9442-aaca99e144db/dqc_reference/reference_markers.fasta -out GCA_005885115.1_ASM588511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:04:14,510] [INFO] Task succeeded: Blastn
[2023-06-28 11:04:14,515] [INFO] Selected 20 target genomes.
[2023-06-28 11:04:14,515] [INFO] Target genome list was writen to GCA_005885115.1_ASM588511v1_genomic.fna/target_genomes.txt
[2023-06-28 11:04:14,520] [INFO] Task started: fastANI
[2023-06-28 11:04:14,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf34dd55-8992-4d33-9132-d8c5c5cb7a3a/GCA_005885115.1_ASM588511v1_genomic.fna.gz --refList GCA_005885115.1_ASM588511v1_genomic.fna/target_genomes.txt --output GCA_005885115.1_ASM588511v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:04:38,461] [INFO] Task succeeded: fastANI
[2023-06-28 11:04:38,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga569e220-2503-4c17-9442-aaca99e144db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:04:38,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga569e220-2503-4c17-9442-aaca99e144db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:04:38,483] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:04:38,483] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 11:04:38,483] [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
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	79.1677	512	845	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	78.8752	405	845	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	78.7925	400	845	95	below_threshold
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	78.6479	422	845	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	78.6277	458	845	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	78.5282	359	845	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	78.4965	365	845	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	78.4856	420	845	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	78.4695	404	845	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	78.4452	446	845	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	78.3641	398	845	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	78.3301	325	845	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	78.3069	362	845	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	78.091	462	845	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	78.0803	466	845	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	78.0199	379	845	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	77.8256	431	845	95	below_threshold
Pilimelia terevasa	strain=JCM 3091	GCA_014647915.1	53372	53372	type	True	77.6921	336	845	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	77.5736	403	845	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	77.4634	401	845	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:04:38,486] [INFO] DFAST Taxonomy check result was written to GCA_005885115.1_ASM588511v1_genomic.fna/tc_result.tsv
[2023-06-28 11:04:38,487] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:04:38,487] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:04:38,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga569e220-2503-4c17-9442-aaca99e144db/dqc_reference/checkm_data
[2023-06-28 11:04:38,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:04:38,528] [INFO] Task started: CheckM
[2023-06-28 11:04:38,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005885115.1_ASM588511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005885115.1_ASM588511v1_genomic.fna/checkm_input GCA_005885115.1_ASM588511v1_genomic.fna/checkm_result
[2023-06-28 11:05:06,111] [INFO] Task succeeded: CheckM
[2023-06-28 11:05:06,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:05:06,135] [INFO] ===== Completeness check finished =====
[2023-06-28 11:05:06,135] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:05:06,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005885115.1_ASM588511v1_genomic.fna/markers.fasta)
[2023-06-28 11:05:06,136] [INFO] Task started: Blastn
[2023-06-28 11:05:06,136] [INFO] Running command: blastn -query GCA_005885115.1_ASM588511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga569e220-2503-4c17-9442-aaca99e144db/dqc_reference/reference_markers_gtdb.fasta -out GCA_005885115.1_ASM588511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:05:07,586] [INFO] Task succeeded: Blastn
[2023-06-28 11:05:07,591] [INFO] Selected 16 target genomes.
[2023-06-28 11:05:07,591] [INFO] Target genome list was writen to GCA_005885115.1_ASM588511v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:05:07,617] [INFO] Task started: fastANI
[2023-06-28 11:05:07,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf34dd55-8992-4d33-9132-d8c5c5cb7a3a/GCA_005885115.1_ASM588511v1_genomic.fna.gz --refList GCA_005885115.1_ASM588511v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005885115.1_ASM588511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:05:27,098] [INFO] Task succeeded: fastANI
[2023-06-28 11:05:27,115] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:05:27,115] [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
GCA_005885115.1	s__Rugosimonospora sp005885115	99.9999	834	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005885555.1	s__Rugosimonospora sp005885555	81.7021	628	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862975.1	s__Rugosimonospora africana	79.1946	509	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	78.5497	409	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900090265.1	s__Micromonospora rifamycinica	78.5331	416	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014764405.1	s__Micromonospora craniellae	78.5079	364	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_014203835.1	s__Micromonospora_H polyrhachis	78.3311	325	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863495.1	s__Micromonospora andamanensis	78.2813	354	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_003751085.1	s__Micromonospora_E sp003751085	78.1838	384	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846275.1	s__Plantactinospora sp002846275	78.1681	418	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	78.1307	458	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647895.1	s__Pilimelia anulata	78.0971	372	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762835.1	s__Plantactinospora sp003762835	78.0737	370	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720385.1	s__Catellatospora vulcania	77.5544	407	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007483665.1	s__Catellatospora sichuanensis	77.4777	399	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015704865.1	s__Actinoplanes sp015704865	77.4365	395	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:05:27,117] [INFO] GTDB search result was written to GCA_005885115.1_ASM588511v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:05:27,118] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:05:27,122] [INFO] DFAST_QC result json was written to GCA_005885115.1_ASM588511v1_genomic.fna/dqc_result.json
[2023-06-28 11:05:27,122] [INFO] DFAST_QC completed!
[2023-06-28 11:05:27,123] [INFO] Total running time: 0h1m24s