[2024-01-25 18:39:50,862] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:50,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:50,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg4267e933-b0ad-426d-8892-93de252e6c66/dqc_reference
[2024-01-25 18:39:51,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:51,992] [INFO] Task started: Prodigal
[2024-01-25 18:39:51,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dc160e1-f7c9-4112-8657-289222d8df22/GCF_016863255.1_ASM1686325v1_genomic.fna.gz | prodigal -d GCF_016863255.1_ASM1686325v1_genomic.fna/cds.fna -a GCF_016863255.1_ASM1686325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:08,121] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:08,122] [INFO] Task started: HMMsearch
[2024-01-25 18:40:08,122] [INFO] Running command: hmmsearch --tblout GCF_016863255.1_ASM1686325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4267e933-b0ad-426d-8892-93de252e6c66/dqc_reference/reference_markers.hmm GCF_016863255.1_ASM1686325v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:08,460] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:08,461] [INFO] Found 6/6 markers.
[2024-01-25 18:40:08,517] [INFO] Query marker FASTA was written to GCF_016863255.1_ASM1686325v1_genomic.fna/markers.fasta
[2024-01-25 18:40:08,517] [INFO] Task started: Blastn
[2024-01-25 18:40:08,517] [INFO] Running command: blastn -query GCF_016863255.1_ASM1686325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4267e933-b0ad-426d-8892-93de252e6c66/dqc_reference/reference_markers.fasta -out GCF_016863255.1_ASM1686325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:09,797] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:09,801] [INFO] Selected 30 target genomes.
[2024-01-25 18:40:09,802] [INFO] Target genome list was writen to GCF_016863255.1_ASM1686325v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:09,821] [INFO] Task started: fastANI
[2024-01-25 18:40:09,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dc160e1-f7c9-4112-8657-289222d8df22/GCF_016863255.1_ASM1686325v1_genomic.fna.gz --refList GCF_016863255.1_ASM1686325v1_genomic.fna/target_genomes.txt --output GCF_016863255.1_ASM1686325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:59,609] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:59,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4267e933-b0ad-426d-8892-93de252e6c66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:59,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4267e933-b0ad-426d-8892-93de252e6c66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:59,626] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:40:59,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:40:59,627] [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
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	79.5335	889	2158	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	79.174	925	2158	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	79.124	940	2158	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	79.1226	844	2158	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	79.0998	927	2158	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	79.0328	917	2158	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	78.9955	944	2158	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	78.9704	900	2158	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	78.8654	900	2158	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8587	812	2158	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.8494	931	2158	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.6581	869	2158	95	below_threshold
Micromonospora echinospora	strain=ATCC 15837	GCA_002266845.1	1877	1877	type	True	78.616	855	2158	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	78.5897	954	2158	95	below_threshold
Micromonospora echinospora	strain=DSM 43816	GCA_900091495.1	1877	1877	type	True	78.5594	878	2158	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	78.5096	966	2158	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	78.4295	842	2158	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	78.3805	937	2158	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	78.3769	1101	2158	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	78.3044	854	2158	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	78.2943	818	2158	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	78.2604	881	2158	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	78.2412	816	2158	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	78.2223	941	2158	95	below_threshold
Virgisporangium aliadipatigenens	strain=NBRC 105644	GCA_016863615.1	741659	741659	type	True	78.0678	924	2158	95	below_threshold
Virgisporangium ochraceum	strain=NBRC 16418	GCA_016863655.1	65505	65505	type	True	78.0461	977	2158	95	below_threshold
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	78.0283	990	2158	95	below_threshold
Longispora fulva	strain=NBRC 105670	GCA_016862835.1	619741	619741	type	True	77.5408	740	2158	95	below_threshold
Longispora fulva	strain=DSM 45356	GCA_015751905.1	619741	619741	type	True	77.5315	739	2158	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.4773	570	2158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:59,628] [INFO] DFAST Taxonomy check result was written to GCF_016863255.1_ASM1686325v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:59,628] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:59,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:59,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4267e933-b0ad-426d-8892-93de252e6c66/dqc_reference/checkm_data
[2024-01-25 18:40:59,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:59,689] [INFO] Task started: CheckM
[2024-01-25 18:40:59,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863255.1_ASM1686325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863255.1_ASM1686325v1_genomic.fna/checkm_input GCF_016863255.1_ASM1686325v1_genomic.fna/checkm_result
[2024-01-25 18:41:50,667] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:50,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:50,759] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:50,759] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:50,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863255.1_ASM1686325v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:50,760] [INFO] Task started: Blastn
[2024-01-25 18:41:50,760] [INFO] Running command: blastn -query GCF_016863255.1_ASM1686325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4267e933-b0ad-426d-8892-93de252e6c66/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863255.1_ASM1686325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:52,777] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:52,780] [INFO] Selected 17 target genomes.
[2024-01-25 18:41:52,780] [INFO] Target genome list was writen to GCF_016863255.1_ASM1686325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:52,789] [INFO] Task started: fastANI
[2024-01-25 18:41:52,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dc160e1-f7c9-4112-8657-289222d8df22/GCF_016863255.1_ASM1686325v1_genomic.fna.gz --refList GCF_016863255.1_ASM1686325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863255.1_ASM1686325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:20,354] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:20,365] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:20,365] [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_016863255.1	s__Planosporangium mesophilum	100.0	2152	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_011947225.1	s__Planosporangium flavigriseum	84.631	1294	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011947195.1	s__Planosporangium thailandense	83.628	1289	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	79.557	883	2158	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_014648395.1	s__Micromonospora fulviviridis	79.1643	928	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900090305.1	s__Micromonospora siamensis	79.1515	840	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	79.1193	923	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_003667505.1	s__Micromonospora sp003667505	78.9885	815	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_900091555.1	s__Micromonospora mirobrigensis	78.8928	895	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348525.1	s__Micromonospora sp004348525	78.8138	774	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885555.1	s__Rugosimonospora sp005885555	78.7906	808	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633685.1	s__Micromonospora_G pisi	78.5485	809	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720365.1	s__Catellatospora paridis	78.3893	851	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751085.1	s__Micromonospora_E sp003751085	78.0941	800	2158	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_016863615.1	s__Virgisporangium aliadipatigenens	78.0761	923	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863635.1	s__Virgisporangium aurantiacum	77.9791	1003	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717135.1	s__Catenuloplanes japonicus	77.8091	855	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catenuloplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:20,368] [INFO] GTDB search result was written to GCF_016863255.1_ASM1686325v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:20,369] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:20,376] [INFO] DFAST_QC result json was written to GCF_016863255.1_ASM1686325v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:20,377] [INFO] DFAST_QC completed!
[2024-01-25 18:42:20,377] [INFO] Total running time: 0h2m30s