[2024-01-24 12:22:37,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,509] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg46ba37e1-598c-47be-b740-ee689e36e9c9/dqc_reference
[2024-01-24 12:22:38,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:38,831] [INFO] Task started: Prodigal
[2024-01-24 12:22:38,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg706aad04-53ad-47d0-9e24-210387632225/GCF_030811375.1_ASM3081137v1_genomic.fna.gz | prodigal -d GCF_030811375.1_ASM3081137v1_genomic.fna/cds.fna -a GCF_030811375.1_ASM3081137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:58,829] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:58,829] [INFO] Task started: HMMsearch
[2024-01-24 12:22:58,830] [INFO] Running command: hmmsearch --tblout GCF_030811375.1_ASM3081137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46ba37e1-598c-47be-b740-ee689e36e9c9/dqc_reference/reference_markers.hmm GCF_030811375.1_ASM3081137v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:59,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:59,158] [INFO] Found 6/6 markers.
[2024-01-24 12:22:59,215] [INFO] Query marker FASTA was written to GCF_030811375.1_ASM3081137v1_genomic.fna/markers.fasta
[2024-01-24 12:22:59,216] [INFO] Task started: Blastn
[2024-01-24 12:22:59,216] [INFO] Running command: blastn -query GCF_030811375.1_ASM3081137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46ba37e1-598c-47be-b740-ee689e36e9c9/dqc_reference/reference_markers.fasta -out GCF_030811375.1_ASM3081137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:00,464] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:00,468] [INFO] Selected 27 target genomes.
[2024-01-24 12:23:00,469] [INFO] Target genome list was writen to GCF_030811375.1_ASM3081137v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:00,486] [INFO] Task started: fastANI
[2024-01-24 12:23:00,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg706aad04-53ad-47d0-9e24-210387632225/GCF_030811375.1_ASM3081137v1_genomic.fna.gz --refList GCF_030811375.1_ASM3081137v1_genomic.fna/target_genomes.txt --output GCF_030811375.1_ASM3081137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:54,663] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:54,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46ba37e1-598c-47be-b740-ee689e36e9c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:54,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46ba37e1-598c-47be-b740-ee689e36e9c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:54,695] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:54,696] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:54,696] [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	80.8419	1373	2181	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	80.5886	1363	2181	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	80.2698	1090	2181	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	80.2538	1184	2181	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	80.1857	1261	2181	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.9804	852	2181	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	79.9478	1332	2181	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	79.8734	1116	2181	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	79.8277	1187	2181	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	79.8255	1142	2181	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	79.8102	1265	2181	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	79.7957	1145	2181	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	79.7818	1261	2181	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	79.7588	1146	2181	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	79.749	1239	2181	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	79.7467	1118	2181	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	79.7408	1274	2181	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	79.7051	931	2181	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.6678	1124	2181	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	79.6158	974	2181	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	79.4799	1200	2181	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	79.4614	1202	2181	95	below_threshold
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	79.2808	1012	2181	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	79.2621	944	2181	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	79.1452	1047	2181	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.4932	746	2181	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.4172	696	2181	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:54,698] [INFO] DFAST Taxonomy check result was written to GCF_030811375.1_ASM3081137v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:54,698] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:54,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:54,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46ba37e1-598c-47be-b740-ee689e36e9c9/dqc_reference/checkm_data
[2024-01-24 12:23:54,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:54,764] [INFO] Task started: CheckM
[2024-01-24 12:23:54,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030811375.1_ASM3081137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030811375.1_ASM3081137v1_genomic.fna/checkm_input GCF_030811375.1_ASM3081137v1_genomic.fna/checkm_result
[2024-01-24 12:25:29,547] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:29,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:29,574] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:29,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:29,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030811375.1_ASM3081137v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:29,575] [INFO] Task started: Blastn
[2024-01-24 12:25:29,575] [INFO] Running command: blastn -query GCF_030811375.1_ASM3081137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46ba37e1-598c-47be-b740-ee689e36e9c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_030811375.1_ASM3081137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:31,478] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:31,484] [INFO] Selected 21 target genomes.
[2024-01-24 12:25:31,484] [INFO] Target genome list was writen to GCF_030811375.1_ASM3081137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:31,500] [INFO] Task started: fastANI
[2024-01-24 12:25:31,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg706aad04-53ad-47d0-9e24-210387632225/GCF_030811375.1_ASM3081137v1_genomic.fna.gz --refList GCF_030811375.1_ASM3081137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030811375.1_ASM3081137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:14,514] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:14,537] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:14,538] [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	99.9799	2135	2181	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	80.8952	1363	2181	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	80.7931	1310	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	80.6794	1168	2181	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	80.6671	1292	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_014205335.1	s__Actinoplanes digitatis	80.5999	1316	2181	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	80.5583	1234	2181	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	80.2624	1180	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_016862115.1	s__Actinoplanes deccanensis	80.0348	1311	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	80.011	1238	2181	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	79.7985	1147	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	79.7881	1136	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_016862375.1	s__Actinoplanes rishiriensis	79.7802	1261	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	79.7202	1282	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	79.7046	1283	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	79.7022	1141	2181	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	79.6931	1253	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	79.605	1177	2181	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	79.5708	981	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217535.1	s__Micromonospora sp004217535	79.539	1066	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018327705.1	s__Catellatospora sp018327705	78.5407	1121	2181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:14,540] [INFO] GTDB search result was written to GCF_030811375.1_ASM3081137v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:14,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:14,545] [INFO] DFAST_QC result json was written to GCF_030811375.1_ASM3081137v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:14,545] [INFO] DFAST_QC completed!
[2024-01-24 12:26:14,545] [INFO] Total running time: 0h3m37s