[2024-01-24 13:18:42,045] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:42,050] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:42,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg841f2938-0eb0-448f-895f-e35635056b7f/dqc_reference
[2024-01-24 13:18:43,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:43,356] [INFO] Task started: Prodigal
[2024-01-24 13:18:43,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg43fbb843-bfbc-4b09-8922-0ff4b7fd16e4/GCF_022229005.1_ASM2222900v1_genomic.fna.gz | prodigal -d GCF_022229005.1_ASM2222900v1_genomic.fna/cds.fna -a GCF_022229005.1_ASM2222900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:04,917] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:04,918] [INFO] Task started: HMMsearch
[2024-01-24 13:19:04,918] [INFO] Running command: hmmsearch --tblout GCF_022229005.1_ASM2222900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg841f2938-0eb0-448f-895f-e35635056b7f/dqc_reference/reference_markers.hmm GCF_022229005.1_ASM2222900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:05,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:05,262] [INFO] Found 6/6 markers.
[2024-01-24 13:19:05,322] [INFO] Query marker FASTA was written to GCF_022229005.1_ASM2222900v1_genomic.fna/markers.fasta
[2024-01-24 13:19:05,322] [INFO] Task started: Blastn
[2024-01-24 13:19:05,322] [INFO] Running command: blastn -query GCF_022229005.1_ASM2222900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg841f2938-0eb0-448f-895f-e35635056b7f/dqc_reference/reference_markers.fasta -out GCF_022229005.1_ASM2222900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:06,444] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:06,447] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:06,447] [INFO] Target genome list was writen to GCF_022229005.1_ASM2222900v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:06,460] [INFO] Task started: fastANI
[2024-01-24 13:19:06,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg43fbb843-bfbc-4b09-8922-0ff4b7fd16e4/GCF_022229005.1_ASM2222900v1_genomic.fna.gz --refList GCF_022229005.1_ASM2222900v1_genomic.fna/target_genomes.txt --output GCF_022229005.1_ASM2222900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:38,959] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:38,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg841f2938-0eb0-448f-895f-e35635056b7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:38,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg841f2938-0eb0-448f-895f-e35635056b7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:38,974] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:38,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:38,975] [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 saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	94.9354	2041	2373	95	below_threshold
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	94.9125	1969	2373	95	below_threshold
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	94.4558	1814	2373	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	94.1574	2035	2373	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	93.9303	1937	2373	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	92.7427	1710	2373	95	below_threshold
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	90.7828	1854	2373	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	90.3849	1831	2373	95	below_threshold
Micromonospora parathelypteridis	strain=CGMCC 4.7347	GCA_014646315.1	1839617	1839617	type	True	90.3495	1837	2373	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	90.1853	1803	2373	95	below_threshold
Micromonospora taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	90.154	1898	2373	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	88.8427	1547	2373	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.1733	1142	2373	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	84.3374	1361	2373	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	84.1906	1070	2373	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.9118	1412	2373	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.8489	1424	2373	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.1669	1360	2373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:38,977] [INFO] DFAST Taxonomy check result was written to GCF_022229005.1_ASM2222900v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:38,977] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:38,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:38,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg841f2938-0eb0-448f-895f-e35635056b7f/dqc_reference/checkm_data
[2024-01-24 13:19:38,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:39,044] [INFO] Task started: CheckM
[2024-01-24 13:19:39,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022229005.1_ASM2222900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022229005.1_ASM2222900v1_genomic.fna/checkm_input GCF_022229005.1_ASM2222900v1_genomic.fna/checkm_result
[2024-01-24 13:20:46,733] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:46,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:46,759] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:46,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:46,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022229005.1_ASM2222900v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:46,761] [INFO] Task started: Blastn
[2024-01-24 13:20:46,761] [INFO] Running command: blastn -query GCF_022229005.1_ASM2222900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg841f2938-0eb0-448f-895f-e35635056b7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_022229005.1_ASM2222900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:48,499] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:48,502] [INFO] Selected 15 target genomes.
[2024-01-24 13:20:48,502] [INFO] Target genome list was writen to GCF_022229005.1_ASM2222900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:48,520] [INFO] Task started: fastANI
[2024-01-24 13:20:48,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg43fbb843-bfbc-4b09-8922-0ff4b7fd16e4/GCF_022229005.1_ASM2222900v1_genomic.fna.gz --refList GCF_022229005.1_ASM2222900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022229005.1_ASM2222900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:16,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:16,533] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:21:16,533] [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_900091575.1	s__Micromonospora saelicesensis	94.9455	2040	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_003264365.1	s__Micromonospora noduli	94.9125	1969	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.92	97.90	0.94	0.91	8	-
GCF_018070325.1	s__Micromonospora sp018070325	94.8484	1905	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_003857035.1	s__Micromonospora arida	94.4547	1815	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.1103	N/A	N/A	N/A	N/A	1	-
GCF_015751785.1	s__Micromonospora vinacea	94.1477	2036	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751765.1	s__Micromonospora ureilytica	93.9403	1936	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	97.34	0.88	0.87	3	-
GCF_003857055.1	s__Micromonospora inaquosa	92.7428	1710	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718555.1	s__Micromonospora chokoriensis_B	92.362	1826	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090275.1	s__Micromonospora zamorensis	90.7764	1854	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.71	96.30	0.91	0.89	6	-
GCF_016907275.1	s__Micromonospora luteifusca	90.1941	1802	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228125.1	s__Micromonospora orduensis	89.2699	1585	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016802865.1	s__Micromonospora sp016802865	89.2246	1487	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297395.2	s__Micromonospora lupini	88.7094	1824	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090305.1	s__Micromonospora siamensis	84.3481	1359	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003857015.1	s__Micromonospora globispora	84.1913	1071	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.52	99.52	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:16,535] [INFO] GTDB search result was written to GCF_022229005.1_ASM2222900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:16,535] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:16,539] [INFO] DFAST_QC result json was written to GCF_022229005.1_ASM2222900v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:16,539] [INFO] DFAST_QC completed!
[2024-01-24 13:21:16,539] [INFO] Total running time: 0h2m34s