[2024-01-24 14:30:34,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg8828e0bf-c48d-41df-bfff-6f5e9f4b493a/dqc_reference
[2024-01-24 14:30:36,187] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:36,188] [INFO] Task started: Prodigal
[2024-01-24 14:30:36,188] [INFO] Running command: gunzip -c /var/lib/cwl/stg354966d9-e4e4-419e-8a8d-0f82bf1c40ec/GCF_006363815.1_ASM636381v1_genomic.fna.gz | prodigal -d GCF_006363815.1_ASM636381v1_genomic.fna/cds.fna -a GCF_006363815.1_ASM636381v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:50,990] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:50,990] [INFO] Task started: HMMsearch
[2024-01-24 14:30:50,990] [INFO] Running command: hmmsearch --tblout GCF_006363815.1_ASM636381v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8828e0bf-c48d-41df-bfff-6f5e9f4b493a/dqc_reference/reference_markers.hmm GCF_006363815.1_ASM636381v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:51,341] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:51,343] [INFO] Found 6/6 markers.
[2024-01-24 14:30:51,401] [INFO] Query marker FASTA was written to GCF_006363815.1_ASM636381v1_genomic.fna/markers.fasta
[2024-01-24 14:30:51,402] [INFO] Task started: Blastn
[2024-01-24 14:30:51,402] [INFO] Running command: blastn -query GCF_006363815.1_ASM636381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8828e0bf-c48d-41df-bfff-6f5e9f4b493a/dqc_reference/reference_markers.fasta -out GCF_006363815.1_ASM636381v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:52,821] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:52,825] [INFO] Selected 23 target genomes.
[2024-01-24 14:30:52,825] [INFO] Target genome list was writen to GCF_006363815.1_ASM636381v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:52,840] [INFO] Task started: fastANI
[2024-01-24 14:30:52,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg354966d9-e4e4-419e-8a8d-0f82bf1c40ec/GCF_006363815.1_ASM636381v1_genomic.fna.gz --refList GCF_006363815.1_ASM636381v1_genomic.fna/target_genomes.txt --output GCF_006363815.1_ASM636381v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:32,365] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:32,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8828e0bf-c48d-41df-bfff-6f5e9f4b493a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:32,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8828e0bf-c48d-41df-bfff-6f5e9f4b493a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:32,388] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:32,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:32,389] [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
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	100.0	1729	1733	95	conclusive
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	84.9402	1244	1733	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	84.7556	1312	1733	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	82.9029	1142	1733	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	81.6023	1040	1733	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	80.8112	1114	1733	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	80.2886	1047	1733	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	80.0931	1000	1733	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	80.0536	1093	1733	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	80.0083	1056	1733	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	79.7507	949	1733	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	79.7477	970	1733	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	79.6388	978	1733	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	79.4209	847	1733	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	79.3649	991	1733	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	79.3504	992	1733	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	78.8044	830	1733	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	78.6053	788	1733	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	78.2642	779	1733	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	76.7724	331	1733	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	76.6659	398	1733	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	76.5703	519	1733	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	76.5283	583	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:32,392] [INFO] DFAST Taxonomy check result was written to GCF_006363815.1_ASM636381v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:32,392] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:32,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:32,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8828e0bf-c48d-41df-bfff-6f5e9f4b493a/dqc_reference/checkm_data
[2024-01-24 14:31:32,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:32,485] [INFO] Task started: CheckM
[2024-01-24 14:31:32,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006363815.1_ASM636381v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006363815.1_ASM636381v1_genomic.fna/checkm_input GCF_006363815.1_ASM636381v1_genomic.fna/checkm_result
[2024-01-24 14:32:49,397] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:49,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:49,423] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:49,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:49,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006363815.1_ASM636381v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:49,425] [INFO] Task started: Blastn
[2024-01-24 14:32:49,425] [INFO] Running command: blastn -query GCF_006363815.1_ASM636381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8828e0bf-c48d-41df-bfff-6f5e9f4b493a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006363815.1_ASM636381v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:51,643] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:51,649] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:51,649] [INFO] Target genome list was writen to GCF_006363815.1_ASM636381v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:51,661] [INFO] Task started: fastANI
[2024-01-24 14:32:51,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg354966d9-e4e4-419e-8a8d-0f82bf1c40ec/GCF_006363815.1_ASM636381v1_genomic.fna.gz --refList GCF_006363815.1_ASM636381v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006363815.1_ASM636381v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:14,862] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:14,881] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:14,881] [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_006363815.1	s__Thermomonospora catenispora	100.0	1729	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003589885.1	s__Thermomonospora amylolytica	90.5393	1459	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCF_000024385.1	s__Thermomonospora curvata	84.9569	1243	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	99.63	99.63	0.99	0.99	2	-
GCF_900108175.1	s__Thermomonospora echinospora	84.7809	1309	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386555.1	s__Thermomonospora umbrina	82.9217	1140	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	81.655	1058	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003289645.1	s__Actinomadura_D craniellae	80.7984	1019	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751755.1	s__Spirillospora viridis	80.782	1121	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718255.1	s__Spirillospora albida	79.8088	942	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348535.1	s__Spirillospora sp004348535	79.6526	898	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105415.1	s__Streptomyces sp900105415	76.7178	584	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_000716445.1	s__Streptomyces wedmorensis	76.6215	608	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCF_014649855.1	s__Streptomyces roseolus	76.5849	616	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911015.1	s__Streptomyces populi	76.5622	569	1733	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:14,883] [INFO] GTDB search result was written to GCF_006363815.1_ASM636381v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:14,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:14,888] [INFO] DFAST_QC result json was written to GCF_006363815.1_ASM636381v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:14,888] [INFO] DFAST_QC completed!
[2024-01-24 14:33:14,888] [INFO] Total running time: 0h2m40s