[2024-01-24 15:02:16,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:16,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:16,998] [INFO] DQC Reference Directory: /var/lib/cwl/stgc98332a8-80f4-402c-85e8-cbc445d03b8b/dqc_reference
[2024-01-24 15:02:18,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:18,310] [INFO] Task started: Prodigal
[2024-01-24 15:02:18,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg57eab1aa-770d-445a-90d4-e84a35751766/GCF_016862955.1_ASM1686295v1_genomic.fna.gz | prodigal -d GCF_016862955.1_ASM1686295v1_genomic.fna/cds.fna -a GCF_016862955.1_ASM1686295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:51,757] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:51,757] [INFO] Task started: HMMsearch
[2024-01-24 15:02:51,758] [INFO] Running command: hmmsearch --tblout GCF_016862955.1_ASM1686295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc98332a8-80f4-402c-85e8-cbc445d03b8b/dqc_reference/reference_markers.hmm GCF_016862955.1_ASM1686295v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:52,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:52,260] [INFO] Found 6/6 markers.
[2024-01-24 15:02:52,353] [INFO] Query marker FASTA was written to GCF_016862955.1_ASM1686295v1_genomic.fna/markers.fasta
[2024-01-24 15:02:52,353] [INFO] Task started: Blastn
[2024-01-24 15:02:52,354] [INFO] Running command: blastn -query GCF_016862955.1_ASM1686295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc98332a8-80f4-402c-85e8-cbc445d03b8b/dqc_reference/reference_markers.fasta -out GCF_016862955.1_ASM1686295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:53,547] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:53,551] [INFO] Selected 21 target genomes.
[2024-01-24 15:02:53,552] [INFO] Target genome list was writen to GCF_016862955.1_ASM1686295v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:53,560] [INFO] Task started: fastANI
[2024-01-24 15:02:53,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg57eab1aa-770d-445a-90d4-e84a35751766/GCF_016862955.1_ASM1686295v1_genomic.fna.gz --refList GCF_016862955.1_ASM1686295v1_genomic.fna/target_genomes.txt --output GCF_016862955.1_ASM1686295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:27,130] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:27,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc98332a8-80f4-402c-85e8-cbc445d03b8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:27,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc98332a8-80f4-402c-85e8-cbc445d03b8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:27,154] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:27,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:27,154] [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
Rhizocola hellebori	strain=NBRC 109834	GCA_016862955.1	1392758	1392758	type	True	100.0	3487	3493	95	conclusive
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	78.7598	1088	3493	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	78.6814	1122	3493	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	78.6532	1103	3493	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	78.595	1100	3493	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	78.5636	1141	3493	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	78.5586	1035	3493	95	below_threshold
Catelliglobosispora koreensis	strain=DSM 44566	GCA_000379685.1	129052	129052	type	True	78.5408	811	3493	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	78.4775	1041	3493	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	77.2594	637	3493	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	77.222	713	3493	95	below_threshold
Salinispora vitiensis	strain=DSM 45548	GCA_000378825.1	999544	999544	type	True	77.0432	410	3493	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	76.8751	805	3493	95	below_threshold
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	76.8148	728	3493	95	below_threshold
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	76.801	752	3493	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	76.7998	739	3493	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	76.7813	717	3493	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	75.7148	326	3493	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	74.9212	65	3493	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	74.8547	64	3493	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	74.7626	64	3493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:27,156] [INFO] DFAST Taxonomy check result was written to GCF_016862955.1_ASM1686295v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:27,156] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:27,157] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:27,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc98332a8-80f4-402c-85e8-cbc445d03b8b/dqc_reference/checkm_data
[2024-01-24 15:03:27,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:27,258] [INFO] Task started: CheckM
[2024-01-24 15:03:27,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862955.1_ASM1686295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862955.1_ASM1686295v1_genomic.fna/checkm_input GCF_016862955.1_ASM1686295v1_genomic.fna/checkm_result
[2024-01-24 15:04:58,700] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:58,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:58,732] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:58,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:58,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862955.1_ASM1686295v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:58,733] [INFO] Task started: Blastn
[2024-01-24 15:04:58,733] [INFO] Running command: blastn -query GCF_016862955.1_ASM1686295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc98332a8-80f4-402c-85e8-cbc445d03b8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862955.1_ASM1686295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:00,590] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:00,593] [INFO] Selected 22 target genomes.
[2024-01-24 15:05:00,593] [INFO] Target genome list was writen to GCF_016862955.1_ASM1686295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:00,611] [INFO] Task started: fastANI
[2024-01-24 15:05:00,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg57eab1aa-770d-445a-90d4-e84a35751766/GCF_016862955.1_ASM1686295v1_genomic.fna.gz --refList GCF_016862955.1_ASM1686295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862955.1_ASM1686295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:34,015] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:34,043] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:34,043] [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_016862955.1	s__Rhizocola hellebori	100.0	3487	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rhizocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003543035.1	s__UBA11056 sp003543035	79.7708	928	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__UBA11056	95.0	99.44	99.44	0.92	0.92	2	-
GCF_016862575.1	s__Catellatospora bangladeshensis	78.74	1111	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_009720365.1	s__Catellatospora paridis	78.7357	1093	3493	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	78.6291	1096	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_009720385.1	s__Catellatospora vulcania	78.5853	1135	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011297335.1	s__Catellatospora methionotrophica	78.5773	1030	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862635.1	s__Catellatospora coxensis	78.5464	1142	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379685.1	s__Catelliglobosispora koreensis	78.5185	816	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catelliglobosispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083965.1	s__Catellatospora sp019083965	78.3123	1062	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204945.1	s__Allocatelliglobosispora scoriae	77.8106	839	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Allocatelliglobosispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	77.5593	646	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003857055.1	s__Micromonospora inaquosa	77.2674	633	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002926165.1	s__Micromonospora chalcea	77.241	708	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_016862275.1	s__Actinoplanes nipponensis	76.8635	810	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205215.1	s__Actinoplanes lobatus	76.8528	750	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_014647795.1	s__Actinoplanes campanulatus	76.8119	729	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_016862395.1	s__Actinoplanes siamensis	76.7013	627	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377865.1	s__WHSY01 sp009377865	75.8036	237	3493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__WHSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909435.1	s__CAIVVT01 sp903909435	74.8212	61	3493	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CAIVVT01	95.0	99.94	99.94	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:34,045] [INFO] GTDB search result was written to GCF_016862955.1_ASM1686295v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:34,045] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:34,050] [INFO] DFAST_QC result json was written to GCF_016862955.1_ASM1686295v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:34,051] [INFO] DFAST_QC completed!
[2024-01-24 15:05:34,051] [INFO] Total running time: 0h3m17s