[2024-01-24 14:46:34,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:34,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:34,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f6aac39-0773-43c2-a2c3-11b181ebadfe/dqc_reference
[2024-01-24 14:46:35,504] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:35,505] [INFO] Task started: Prodigal
[2024-01-24 14:46:35,505] [INFO] Running command: gunzip -c /var/lib/cwl/stge1bd1296-a57b-4f37-9b45-61406a7a56db/GCF_014204945.1_ASM1420494v1_genomic.fna.gz | prodigal -d GCF_014204945.1_ASM1420494v1_genomic.fna/cds.fna -a GCF_014204945.1_ASM1420494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:01,194] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:01,195] [INFO] Task started: HMMsearch
[2024-01-24 14:47:01,195] [INFO] Running command: hmmsearch --tblout GCF_014204945.1_ASM1420494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f6aac39-0773-43c2-a2c3-11b181ebadfe/dqc_reference/reference_markers.hmm GCF_014204945.1_ASM1420494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:01,644] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:01,646] [INFO] Found 6/6 markers.
[2024-01-24 14:47:01,727] [INFO] Query marker FASTA was written to GCF_014204945.1_ASM1420494v1_genomic.fna/markers.fasta
[2024-01-24 14:47:01,727] [INFO] Task started: Blastn
[2024-01-24 14:47:01,728] [INFO] Running command: blastn -query GCF_014204945.1_ASM1420494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f6aac39-0773-43c2-a2c3-11b181ebadfe/dqc_reference/reference_markers.fasta -out GCF_014204945.1_ASM1420494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:02,951] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:02,955] [INFO] Selected 23 target genomes.
[2024-01-24 14:47:02,956] [INFO] Target genome list was writen to GCF_014204945.1_ASM1420494v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:02,982] [INFO] Task started: fastANI
[2024-01-24 14:47:02,983] [INFO] Running command: fastANI --query /var/lib/cwl/stge1bd1296-a57b-4f37-9b45-61406a7a56db/GCF_014204945.1_ASM1420494v1_genomic.fna.gz --refList GCF_014204945.1_ASM1420494v1_genomic.fna/target_genomes.txt --output GCF_014204945.1_ASM1420494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:44,269] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:44,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f6aac39-0773-43c2-a2c3-11b181ebadfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:44,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f6aac39-0773-43c2-a2c3-11b181ebadfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:44,292] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:44,293] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:44,293] [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	79.5	1315	3048	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	79.3178	1303	3048	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	79.2268	1314	3048	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	79.1997	1296	3048	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	79.1957	1277	3048	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	79.1901	1266	3048	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	79.1866	1281	3048	95	below_threshold
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	79.0511	1310	3048	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.4265	745	3048	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	78.3641	745	3048	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.3605	832	3048	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	78.2271	1004	3048	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.1825	1002	3048	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	78.1519	972	3048	95	below_threshold
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	78.0434	816	3048	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	77.9248	837	3048	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	77.8063	1012	3048	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	77.7891	1007	3048	95	below_threshold
Rhizocola hellebori	strain=NBRC 109834	GCA_016862955.1	1392758	1392758	type	True	77.6851	881	3048	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	77.6653	1122	3048	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	77.5315	989	3048	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	77.3483	955	3048	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	77.2254	759	3048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:44,295] [INFO] DFAST Taxonomy check result was written to GCF_014204945.1_ASM1420494v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:44,295] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:44,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:44,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f6aac39-0773-43c2-a2c3-11b181ebadfe/dqc_reference/checkm_data
[2024-01-24 14:47:44,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:44,383] [INFO] Task started: CheckM
[2024-01-24 14:47:44,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204945.1_ASM1420494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204945.1_ASM1420494v1_genomic.fna/checkm_input GCF_014204945.1_ASM1420494v1_genomic.fna/checkm_result
[2024-01-24 14:49:04,728] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:04,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:04,758] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:04,759] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:04,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204945.1_ASM1420494v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:04,760] [INFO] Task started: Blastn
[2024-01-24 14:49:04,760] [INFO] Running command: blastn -query GCF_014204945.1_ASM1420494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f6aac39-0773-43c2-a2c3-11b181ebadfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204945.1_ASM1420494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:06,874] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:06,877] [INFO] Selected 18 target genomes.
[2024-01-24 14:49:06,877] [INFO] Target genome list was writen to GCF_014204945.1_ASM1420494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:06,895] [INFO] Task started: fastANI
[2024-01-24 14:49:06,896] [INFO] Running command: fastANI --query /var/lib/cwl/stge1bd1296-a57b-4f37-9b45-61406a7a56db/GCF_014204945.1_ASM1420494v1_genomic.fna.gz --refList GCF_014204945.1_ASM1420494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204945.1_ASM1420494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:44,965] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:44,985] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:44,986] [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_014204945.1	s__Allocatelliglobosispora scoriae	100.0	3048	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Allocatelliglobosispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009720385.1	s__Catellatospora vulcania	79.5009	1316	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	79.3017	1293	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_007483665.1	s__Catellatospora sichuanensis	79.2662	1319	3048	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	79.233	1267	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003610235.1	s__Catellatospora citrea	79.2162	1322	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_009720365.1	s__Catellatospora paridis	79.2161	1294	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862635.1	s__Catellatospora coxensis	79.1054	1294	3048	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	79.0186	1319	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428945.1	s__Hamadaea tsunoensis	78.9568	1270	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362815.1	s__Hamadaea sp013362815	78.5766	970	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091605.1	s__Micromonospora tulbaghiae	78.0407	948	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_004348525.1	s__Micromonospora sp004348525	78.0265	852	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324255.1	s__Polymorphospora rubra	78.0017	1022	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862915.1	s__Plantactinospora endophytica	77.8359	1020	3048	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	77.684	966	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885555.1	s__Rugosimonospora sp005885555	77.1114	752	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862975.1	s__Rugosimonospora africana	77.0361	878	3048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:44,987] [INFO] GTDB search result was written to GCF_014204945.1_ASM1420494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:44,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:44,994] [INFO] DFAST_QC result json was written to GCF_014204945.1_ASM1420494v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:44,994] [INFO] DFAST_QC completed!
[2024-01-24 14:49:44,994] [INFO] Total running time: 0h3m11s