[2024-01-24 13:18:30,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:30,140] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:30,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1d7e333-a098-4c30-9ad5-8b9cf3ce35a9/dqc_reference
[2024-01-24 13:18:31,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:31,430] [INFO] Task started: Prodigal
[2024-01-24 13:18:31,430] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa2bf820-5240-4fa5-becd-826c5430e47e/GCF_000428945.1_ASM42894v1_genomic.fna.gz | prodigal -d GCF_000428945.1_ASM42894v1_genomic.fna/cds.fna -a GCF_000428945.1_ASM42894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:56,810] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:56,810] [INFO] Task started: HMMsearch
[2024-01-24 13:18:56,811] [INFO] Running command: hmmsearch --tblout GCF_000428945.1_ASM42894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1d7e333-a098-4c30-9ad5-8b9cf3ce35a9/dqc_reference/reference_markers.hmm GCF_000428945.1_ASM42894v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:57,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:57,341] [INFO] Found 6/6 markers.
[2024-01-24 13:18:57,416] [INFO] Query marker FASTA was written to GCF_000428945.1_ASM42894v1_genomic.fna/markers.fasta
[2024-01-24 13:18:57,416] [INFO] Task started: Blastn
[2024-01-24 13:18:57,416] [INFO] Running command: blastn -query GCF_000428945.1_ASM42894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1d7e333-a098-4c30-9ad5-8b9cf3ce35a9/dqc_reference/reference_markers.fasta -out GCF_000428945.1_ASM42894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:58,779] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:58,782] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:58,783] [INFO] Target genome list was writen to GCF_000428945.1_ASM42894v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:59,649] [INFO] Task started: fastANI
[2024-01-24 13:18:59,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa2bf820-5240-4fa5-becd-826c5430e47e/GCF_000428945.1_ASM42894v1_genomic.fna.gz --refList GCF_000428945.1_ASM42894v1_genomic.fna/target_genomes.txt --output GCF_000428945.1_ASM42894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:36,743] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:36,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1d7e333-a098-4c30-9ad5-8b9cf3ce35a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:36,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1d7e333-a098-4c30-9ad5-8b9cf3ce35a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:36,765] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:36,765] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:36,765] [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
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	78.7628	1279	3127	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	78.7195	1228	3127	95	below_threshold
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	78.7117	1224	3127	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	78.6376	1243	3127	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	78.5818	1276	3127	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	78.5392	1212	3127	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	78.5282	1198	3127	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	78.5134	1279	3127	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	78.1343	1007	3127	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	78.1307	970	3127	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	78.1221	1006	3127	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	78.117	888	3127	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	78.1153	988	3127	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	78.1091	1015	3127	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	78.0687	830	3127	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	78.0238	1018	3127	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	77.9919	863	3127	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	77.8552	918	3127	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	77.8277	1035	3127	95	below_threshold
Micromonospora chokoriensis	strain=DSM 45160	GCA_900091505.1	356851	356851	type	True	77.782	894	3127	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	77.7776	1002	3127	95	below_threshold
Micromonospora taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	77.766	913	3127	95	below_threshold
Allorhizocola rhizosphaerae	strain=CPCC 204380	GCA_003426775.1	1872709	1872709	type	True	77.4548	720	3127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:36,767] [INFO] DFAST Taxonomy check result was written to GCF_000428945.1_ASM42894v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:36,768] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:36,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:36,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1d7e333-a098-4c30-9ad5-8b9cf3ce35a9/dqc_reference/checkm_data
[2024-01-24 13:19:36,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:36,862] [INFO] Task started: CheckM
[2024-01-24 13:19:36,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428945.1_ASM42894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428945.1_ASM42894v1_genomic.fna/checkm_input GCF_000428945.1_ASM42894v1_genomic.fna/checkm_result
[2024-01-24 13:20:56,843] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:56,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:56,870] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:56,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:56,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428945.1_ASM42894v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:56,871] [INFO] Task started: Blastn
[2024-01-24 13:20:56,872] [INFO] Running command: blastn -query GCF_000428945.1_ASM42894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1d7e333-a098-4c30-9ad5-8b9cf3ce35a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428945.1_ASM42894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:58,778] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:58,782] [INFO] Selected 19 target genomes.
[2024-01-24 13:20:58,783] [INFO] Target genome list was writen to GCF_000428945.1_ASM42894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:58,960] [INFO] Task started: fastANI
[2024-01-24 13:20:58,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa2bf820-5240-4fa5-becd-826c5430e47e/GCF_000428945.1_ASM42894v1_genomic.fna.gz --refList GCF_000428945.1_ASM42894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428945.1_ASM42894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:38,960] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:38,975] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:38,976] [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_000428945.1	s__Hamadaea tsunoensis	100.0	3121	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013362815.1	s__Hamadaea sp013362815	80.4327	1327	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361475.1	s__Hamadaea sp013361475	80.4029	1107	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	99.33	99.31	0.83	0.82	3	-
GCF_014204945.1	s__Allocatelliglobosispora scoriae	78.8949	1263	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Allocatelliglobosispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	78.8008	1281	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_016862635.1	s__Catellatospora coxensis	78.7949	1283	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018327705.1	s__Catellatospora sp018327705	78.7908	1347	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720385.1	s__Catellatospora vulcania	78.763	1276	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083965.1	s__Catellatospora sp019083965	78.7169	1229	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003610235.1	s__Catellatospora citrea	78.5857	1288	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_011297335.1	s__Catellatospora methionotrophica	78.5605	1205	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900091565.1	s__Micromonospora marina	78.1119	890	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.96	0.90	0.86	3	-
GCF_900090105.1	s__Micromonospora humi	78.1112	990	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091605.1	s__Micromonospora tulbaghiae	78.1099	975	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_000145235.1	s__Micromonospora aurantiaca	78.0688	1026	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	98.37	95.58	0.90	0.84	15	-
GCF_003172955.1	s__Micromonospora sp003172955	77.993	865	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	77.9161	1000	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803395.1	s__Micromonospora sp016803395	77.81	851	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	77.7535	1010	3127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:38,977] [INFO] GTDB search result was written to GCF_000428945.1_ASM42894v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:38,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:38,982] [INFO] DFAST_QC result json was written to GCF_000428945.1_ASM42894v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:38,983] [INFO] DFAST_QC completed!
[2024-01-24 13:21:38,983] [INFO] Total running time: 0h3m9s