[2024-01-24 11:52:04,831] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg1152f95d-4c74-485e-ac32-9f39112b33a9/dqc_reference
[2024-01-24 11:52:06,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:06,059] [INFO] Task started: Prodigal
[2024-01-24 11:52:06,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg13933e8a-0169-4768-84e0-8fbc4c48c87e/GCF_018324255.1_ASM1832425v1_genomic.fna.gz | prodigal -d GCF_018324255.1_ASM1832425v1_genomic.fna/cds.fna -a GCF_018324255.1_ASM1832425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:53,203] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:53,204] [INFO] Task started: HMMsearch
[2024-01-24 11:52:53,204] [INFO] Running command: hmmsearch --tblout GCF_018324255.1_ASM1832425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1152f95d-4c74-485e-ac32-9f39112b33a9/dqc_reference/reference_markers.hmm GCF_018324255.1_ASM1832425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:53,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:53,559] [INFO] Found 6/6 markers.
[2024-01-24 11:52:53,798] [INFO] Query marker FASTA was written to GCF_018324255.1_ASM1832425v1_genomic.fna/markers.fasta
[2024-01-24 11:52:53,798] [INFO] Task started: Blastn
[2024-01-24 11:52:53,798] [INFO] Running command: blastn -query GCF_018324255.1_ASM1832425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1152f95d-4c74-485e-ac32-9f39112b33a9/dqc_reference/reference_markers.fasta -out GCF_018324255.1_ASM1832425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:55,070] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:55,073] [INFO] Selected 31 target genomes.
[2024-01-24 11:52:55,074] [INFO] Target genome list was writen to GCF_018324255.1_ASM1832425v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:55,087] [INFO] Task started: fastANI
[2024-01-24 11:52:55,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg13933e8a-0169-4768-84e0-8fbc4c48c87e/GCF_018324255.1_ASM1832425v1_genomic.fna.gz --refList GCF_018324255.1_ASM1832425v1_genomic.fna/target_genomes.txt --output GCF_018324255.1_ASM1832425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:52,437] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:52,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1152f95d-4c74-485e-ac32-9f39112b33a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:52,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1152f95d-4c74-485e-ac32-9f39112b33a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:52,463] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:53:52,463] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:53:52,464] [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 echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	81.265	1329	2788	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	81.2397	934	2788	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	81.1692	1036	2788	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	81.0944	1289	2788	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	81.0701	1222	2788	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	81.0305	1305	2788	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	81.0178	1273	2788	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	80.9256	1346	2788	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	80.918	951	2788	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	80.8645	1218	2788	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	80.769	1159	2788	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	80.7633	1222	2788	95	below_threshold
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	80.7544	1130	2788	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	80.7479	1077	2788	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	80.7293	1068	2788	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	80.7198	1267	2788	95	below_threshold
Micromonospora yangpuensis	strain=CGMCC 4.5736	GCA_014645775.1	683228	683228	type	True	80.708	1119	2788	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	80.7054	1279	2788	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	80.6382	1140	2788	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	80.6174	1246	2788	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	80.5898	1236	2788	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	80.5473	1219	2788	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	80.5174	1208	2788	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	80.476	1130	2788	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	80.2482	1249	2788	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	79.7052	1354	2788	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	79.339	1198	2788	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	79.3381	1203	2788	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	78.3365	1140	2788	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	78.2745	1148	2788	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.8782	1301	2788	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:52,466] [INFO] DFAST Taxonomy check result was written to GCF_018324255.1_ASM1832425v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:52,466] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:52,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:52,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1152f95d-4c74-485e-ac32-9f39112b33a9/dqc_reference/checkm_data
[2024-01-24 11:53:52,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:52,547] [INFO] Task started: CheckM
[2024-01-24 11:53:52,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018324255.1_ASM1832425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018324255.1_ASM1832425v1_genomic.fna/checkm_input GCF_018324255.1_ASM1832425v1_genomic.fna/checkm_result
[2024-01-24 11:57:02,608] [INFO] Task succeeded: CheckM
[2024-01-24 11:57:02,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:57:02,639] [INFO] ===== Completeness check finished =====
[2024-01-24 11:57:02,639] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:57:02,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018324255.1_ASM1832425v1_genomic.fna/markers.fasta)
[2024-01-24 11:57:02,640] [INFO] Task started: Blastn
[2024-01-24 11:57:02,640] [INFO] Running command: blastn -query GCF_018324255.1_ASM1832425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1152f95d-4c74-485e-ac32-9f39112b33a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_018324255.1_ASM1832425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:57:04,544] [INFO] Task succeeded: Blastn
[2024-01-24 11:57:04,559] [INFO] Selected 25 target genomes.
[2024-01-24 11:57:04,559] [INFO] Target genome list was writen to GCF_018324255.1_ASM1832425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:57:04,583] [INFO] Task started: fastANI
[2024-01-24 11:57:04,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg13933e8a-0169-4768-84e0-8fbc4c48c87e/GCF_018324255.1_ASM1832425v1_genomic.fna.gz --refList GCF_018324255.1_ASM1832425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018324255.1_ASM1832425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:57:51,807] [INFO] Task succeeded: fastANI
[2024-01-24 11:57:51,844] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:57:51,844] [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_018324255.1	s__Polymorphospora rubra	100.0	2788	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900091445.1	s__Micromonospora echinofusca	81.2836	1328	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.23	97.23	0.90	0.90	2	-
GCF_003434305.1	s__Micromonospora sp003434305	81.2193	1279	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345505.1	s__Micromonospora sp004345505	81.1523	1345	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.85	96.85	0.87	0.87	2	-
GCF_900090295.1	s__Micromonospora coxensis	81.1347	1281	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	81.0961	1047	2788	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_902825405.1	s__Micromonospora maritima	81.075	929	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090315.1	s__Micromonospora citrea	81.0082	1303	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	80.9189	1349	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	80.9175	1294	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	80.8269	1225	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_017614955.1	s__Micromonospora echinofusca_A	80.8223	1172	2788	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	80.7538	1125	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	80.7136	1230	2788	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	80.681	1085	2788	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_900090265.1	s__Micromonospora rifamycinica	80.619	1224	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000982955.1	s__Micromonospora sp000982955	80.5747	1167	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862935.1	s__Plantactinospora mayteni	80.5662	1353	2788	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	80.49	1418	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228125.1	s__Micromonospora orduensis	80.4809	1129	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846275.1	s__Plantactinospora sp002846275	80.4808	1281	2788	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	80.1956	1347	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015690345.1	s__Plantactinospora sp015690345	80.0998	1161	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107455.1	s__Asanoa ishikariensis	79.3143	1208	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	78.1006	1174	2788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:57:51,847] [INFO] GTDB search result was written to GCF_018324255.1_ASM1832425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:57:51,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:57:51,854] [INFO] DFAST_QC result json was written to GCF_018324255.1_ASM1832425v1_genomic.fna/dqc_result.json
[2024-01-24 11:57:51,855] [INFO] DFAST_QC completed!
[2024-01-24 11:57:51,855] [INFO] Total running time: 0h5m47s