[2024-01-25 19:38:20,359] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:20,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:20,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a3851c0-765f-441b-a342-3340af12adf2/dqc_reference
[2024-01-25 19:38:21,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:21,567] [INFO] Task started: Prodigal
[2024-01-25 19:38:21,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b0184c1-febb-4bc0-952a-710765cb1a9d/GCF_016863475.1_ASM1686347v1_genomic.fna.gz | prodigal -d GCF_016863475.1_ASM1686347v1_genomic.fna/cds.fna -a GCF_016863475.1_ASM1686347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:37,102] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:37,102] [INFO] Task started: HMMsearch
[2024-01-25 19:38:37,102] [INFO] Running command: hmmsearch --tblout GCF_016863475.1_ASM1686347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a3851c0-765f-441b-a342-3340af12adf2/dqc_reference/reference_markers.hmm GCF_016863475.1_ASM1686347v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:37,428] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:37,429] [INFO] Found 6/6 markers.
[2024-01-25 19:38:37,485] [INFO] Query marker FASTA was written to GCF_016863475.1_ASM1686347v1_genomic.fna/markers.fasta
[2024-01-25 19:38:37,486] [INFO] Task started: Blastn
[2024-01-25 19:38:37,486] [INFO] Running command: blastn -query GCF_016863475.1_ASM1686347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a3851c0-765f-441b-a342-3340af12adf2/dqc_reference/reference_markers.fasta -out GCF_016863475.1_ASM1686347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:38,728] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:38,731] [INFO] Selected 27 target genomes.
[2024-01-25 19:38:38,731] [INFO] Target genome list was writen to GCF_016863475.1_ASM1686347v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:38,745] [INFO] Task started: fastANI
[2024-01-25 19:38:38,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0184c1-febb-4bc0-952a-710765cb1a9d/GCF_016863475.1_ASM1686347v1_genomic.fna.gz --refList GCF_016863475.1_ASM1686347v1_genomic.fna/target_genomes.txt --output GCF_016863475.1_ASM1686347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:31,706] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:31,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a3851c0-765f-441b-a342-3340af12adf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:31,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a3851c0-765f-441b-a342-3340af12adf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:31,722] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:39:31,722] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:39:31,722] [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
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	80.9505	1344	2140	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	80.5425	1358	2140	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	80.289	1096	2140	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	80.2177	1178	2140	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	80.0944	1250	2140	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	80.0704	1268	2140	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.9497	860	2140	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	79.8834	1118	2140	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	79.8691	1122	2140	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	79.8438	1100	2140	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	79.8263	1125	2140	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	79.8252	1118	2140	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	79.772	1177	2140	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	79.7653	1275	2140	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	79.7645	1267	2140	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	79.7529	1228	2140	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	79.7437	1270	2140	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.7091	1105	2140	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	79.6511	977	2140	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	79.636	927	2140	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	79.4195	1199	2140	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	79.4093	1185	2140	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	79.3431	937	2140	95	below_threshold
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	79.3371	1001	2140	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	79.2782	1013	2140	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.4681	722	2140	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.4037	667	2140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:31,723] [INFO] DFAST Taxonomy check result was written to GCF_016863475.1_ASM1686347v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:31,723] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:31,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:31,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a3851c0-765f-441b-a342-3340af12adf2/dqc_reference/checkm_data
[2024-01-25 19:39:31,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:31,784] [INFO] Task started: CheckM
[2024-01-25 19:39:31,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863475.1_ASM1686347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863475.1_ASM1686347v1_genomic.fna/checkm_input GCF_016863475.1_ASM1686347v1_genomic.fna/checkm_result
[2024-01-25 19:40:44,071] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:44,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:44,096] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:44,097] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:44,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863475.1_ASM1686347v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:44,098] [INFO] Task started: Blastn
[2024-01-25 19:40:44,098] [INFO] Running command: blastn -query GCF_016863475.1_ASM1686347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a3851c0-765f-441b-a342-3340af12adf2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863475.1_ASM1686347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:46,070] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:46,073] [INFO] Selected 21 target genomes.
[2024-01-25 19:40:46,073] [INFO] Target genome list was writen to GCF_016863475.1_ASM1686347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:46,084] [INFO] Task started: fastANI
[2024-01-25 19:40:46,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0184c1-febb-4bc0-952a-710765cb1a9d/GCF_016863475.1_ASM1686347v1_genomic.fna.gz --refList GCF_016863475.1_ASM1686347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863475.1_ASM1686347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:29,132] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:29,145] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:29,146] [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_016863475.1	s__Spirilliplanes yamanashiensis	100.0	2138	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862275.1	s__Actinoplanes nipponensis	80.9839	1337	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464385.1	s__Actinoplanes sp016464385	80.7943	1290	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	80.6948	1281	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	80.6434	1143	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205335.1	s__Actinoplanes digitatis	80.6062	1310	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014648355.1	s__Actinoplanes azureus	80.518	1215	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751945.1	s__Actinoplanes caeruleus	80.2091	1181	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000389965.1	s__Actinoplanes sp000389965	80.0542	1214	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	79.9498	1297	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	79.8949	1117	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_016862395.1	s__Actinoplanes siamensis	79.8069	1120	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	79.7938	1130	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	79.7497	1279	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721705.1	s__Actinoplanes subtropicus	79.7479	1228	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217535.1	s__Micromonospora sp004217535	79.7475	1020	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862375.1	s__Actinoplanes rishiriensis	79.7273	1275	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228125.1	s__Micromonospora orduensis	79.6928	968	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	79.6816	1283	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003999975.1	s__Actinoplanes sp003999975	79.4683	1196	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018327705.1	s__Catellatospora sp018327705	78.5159	1090	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:29,148] [INFO] GTDB search result was written to GCF_016863475.1_ASM1686347v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:29,149] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:29,153] [INFO] DFAST_QC result json was written to GCF_016863475.1_ASM1686347v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:29,153] [INFO] DFAST_QC completed!
[2024-01-25 19:41:29,153] [INFO] Total running time: 0h3m9s