[2024-01-24 12:44:11,245] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,250] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,250] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8a6598b-8108-4993-b351-380c2fc234be/dqc_reference
[2024-01-24 12:44:12,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,644] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,644] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6263c7d-7eed-43d4-8f2d-2ff2c46d3365/GCF_016862935.1_ASM1686293v1_genomic.fna.gz | prodigal -d GCF_016862935.1_ASM1686293v1_genomic.fna/cds.fna -a GCF_016862935.1_ASM1686293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:38,831] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:38,832] [INFO] Task started: HMMsearch
[2024-01-24 12:44:38,832] [INFO] Running command: hmmsearch --tblout GCF_016862935.1_ASM1686293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8a6598b-8108-4993-b351-380c2fc234be/dqc_reference/reference_markers.hmm GCF_016862935.1_ASM1686293v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:39,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:39,326] [INFO] Found 6/6 markers.
[2024-01-24 12:44:39,399] [INFO] Query marker FASTA was written to GCF_016862935.1_ASM1686293v1_genomic.fna/markers.fasta
[2024-01-24 12:44:39,399] [INFO] Task started: Blastn
[2024-01-24 12:44:39,399] [INFO] Running command: blastn -query GCF_016862935.1_ASM1686293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8a6598b-8108-4993-b351-380c2fc234be/dqc_reference/reference_markers.fasta -out GCF_016862935.1_ASM1686293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:40,557] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:40,560] [INFO] Selected 31 target genomes.
[2024-01-24 12:44:40,561] [INFO] Target genome list was writen to GCF_016862935.1_ASM1686293v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:40,583] [INFO] Task started: fastANI
[2024-01-24 12:44:40,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6263c7d-7eed-43d4-8f2d-2ff2c46d3365/GCF_016862935.1_ASM1686293v1_genomic.fna.gz --refList GCF_016862935.1_ASM1686293v1_genomic.fna/target_genomes.txt --output GCF_016862935.1_ASM1686293v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:35,084] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:35,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8a6598b-8108-4993-b351-380c2fc234be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:35,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8a6598b-8108-4993-b351-380c2fc234be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:35,110] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:35,110] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:35,111] [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 phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	81.6426	985	3217	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	81.5177	1250	3217	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	81.2606	1317	3217	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	81.2347	1177	3217	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	81.1949	1297	3217	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	81.1677	1236	3217	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	81.1533	1262	3217	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	81.1211	982	3217	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	81.1191	1217	3217	95	below_threshold
Micromonospora sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	81.1186	1271	3217	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	81.1117	1211	3217	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	81.0504	1190	3217	95	below_threshold
Micromonospora inyonensis	strain=DSM 46123	GCA_900091415.1	47866	47866	type	True	81.0475	1177	3217	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	81.0356	1314	3217	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	80.8329	1089	3217	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	80.8033	1210	3217	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	80.7928	1330	3217	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	80.749	1203	3217	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	80.7178	1348	3217	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	80.6876	1255	3217	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	80.6385	1314	3217	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	80.6264	1198	3217	95	below_threshold
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	80.6188	1205	3217	95	below_threshold
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	80.6121	1309	3217	95	below_threshold
Micromonospora chokoriensis	strain=DSM 45160	GCA_900091505.1	356851	356851	type	True	80.5957	1241	3217	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	80.5458	1212	3217	95	below_threshold
Micromonospora taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	80.474	1300	3217	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	79.5185	1451	3217	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	79.3179	1396	3217	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	79.2979	1291	3217	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	78.1734	1226	3217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:35,112] [INFO] DFAST Taxonomy check result was written to GCF_016862935.1_ASM1686293v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:35,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:35,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:35,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8a6598b-8108-4993-b351-380c2fc234be/dqc_reference/checkm_data
[2024-01-24 12:45:35,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:35,207] [INFO] Task started: CheckM
[2024-01-24 12:45:35,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862935.1_ASM1686293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862935.1_ASM1686293v1_genomic.fna/checkm_input GCF_016862935.1_ASM1686293v1_genomic.fna/checkm_result
[2024-01-24 12:46:54,330] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:54,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:54,361] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:54,361] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:54,362] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862935.1_ASM1686293v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:54,362] [INFO] Task started: Blastn
[2024-01-24 12:46:54,363] [INFO] Running command: blastn -query GCF_016862935.1_ASM1686293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8a6598b-8108-4993-b351-380c2fc234be/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862935.1_ASM1686293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:56,084] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:56,088] [INFO] Selected 14 target genomes.
[2024-01-24 12:46:56,088] [INFO] Target genome list was writen to GCF_016862935.1_ASM1686293v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:56,103] [INFO] Task started: fastANI
[2024-01-24 12:46:56,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6263c7d-7eed-43d4-8f2d-2ff2c46d3365/GCF_016862935.1_ASM1686293v1_genomic.fna.gz --refList GCF_016862935.1_ASM1686293v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862935.1_ASM1686293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:25,615] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:25,627] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:25,627] [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_016862935.1	s__Plantactinospora mayteni	100.0	3212	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003030345.1	s__Plantactinospora sp003030345	91.2482	2093	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_002846275.1	s__Plantactinospora sp002846275	90.1017	1989	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217235.1	s__Plantactinospora sp004217235	90.0844	1892	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862915.1	s__Plantactinospora endophytica	90.0767	2266	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874095.1	s__Plantactinospora soyae	85.907	2116	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016802835.1	s__Micromonospora sp016802835	81.6402	932	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	81.3384	1197	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	81.2559	1318	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	81.116	1214	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	81.0849	988	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567585.1	s__Micromonospora rosaria	81.0733	1306	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203835.1	s__Micromonospora_H polyrhachis	80.7236	1207	3217	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	80.4786	1186	3217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:25,629] [INFO] GTDB search result was written to GCF_016862935.1_ASM1686293v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:25,630] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:25,639] [INFO] DFAST_QC result json was written to GCF_016862935.1_ASM1686293v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:25,639] [INFO] DFAST_QC completed!
[2024-01-24 12:47:25,639] [INFO] Total running time: 0h3m14s