[2024-01-24 15:18:38,878] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg05a09046-f1b2-4be2-b9e9-c211bcb10a5a/dqc_reference
[2024-01-24 15:18:40,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,224] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg8df0b36b-9ca2-44af-8691-2f177d1792e2/GCF_003633685.1_ASM363368v1_genomic.fna.gz | prodigal -d GCF_003633685.1_ASM363368v1_genomic.fna/cds.fna -a GCF_003633685.1_ASM363368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:10,461] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:10,461] [INFO] Task started: HMMsearch
[2024-01-24 15:19:10,461] [INFO] Running command: hmmsearch --tblout GCF_003633685.1_ASM363368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05a09046-f1b2-4be2-b9e9-c211bcb10a5a/dqc_reference/reference_markers.hmm GCF_003633685.1_ASM363368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:10,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:10,923] [INFO] Found 6/6 markers.
[2024-01-24 15:19:10,991] [INFO] Query marker FASTA was written to GCF_003633685.1_ASM363368v1_genomic.fna/markers.fasta
[2024-01-24 15:19:10,992] [INFO] Task started: Blastn
[2024-01-24 15:19:10,992] [INFO] Running command: blastn -query GCF_003633685.1_ASM363368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05a09046-f1b2-4be2-b9e9-c211bcb10a5a/dqc_reference/reference_markers.fasta -out GCF_003633685.1_ASM363368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:12,263] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:12,266] [INFO] Selected 33 target genomes.
[2024-01-24 15:19:12,266] [INFO] Target genome list was writen to GCF_003633685.1_ASM363368v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:12,279] [INFO] Task started: fastANI
[2024-01-24 15:19:12,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg8df0b36b-9ca2-44af-8691-2f177d1792e2/GCF_003633685.1_ASM363368v1_genomic.fna.gz --refList GCF_003633685.1_ASM363368v1_genomic.fna/target_genomes.txt --output GCF_003633685.1_ASM363368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:04,308] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:04,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05a09046-f1b2-4be2-b9e9-c211bcb10a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:04,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05a09046-f1b2-4be2-b9e9-c211bcb10a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:04,338] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:20:04,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:20:04,339] [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
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	81.5709	950	2913	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	81.5609	1199	2913	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	81.3886	1260	2913	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	81.3623	1193	2913	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	81.3074	1171	2913	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	81.2271	1135	2913	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	81.1974	1245	2913	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	81.0715	1032	2913	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	81.0645	1098	2913	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	81.0341	1175	2913	95	below_threshold
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	80.9892	1219	2913	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	80.9385	1260	2913	95	below_threshold
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	80.9204	1213	2913	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	80.8986	1273	2913	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	80.8853	1287	2913	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	80.8431	1277	2913	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	80.8326	1108	2913	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	80.8266	1249	2913	95	below_threshold
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	80.8169	1149	2913	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	80.7353	1028	2913	95	below_threshold
Micromonospora yangpuensis	strain=CGMCC 4.5736	GCA_014645775.1	683228	683228	type	True	80.7234	1124	2913	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	80.6887	1229	2913	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	80.6861	1127	2913	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	80.6717	1098	2913	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	80.6567	1153	2913	95	below_threshold
Micromonospora costi	strain=CS1-12	GCA_003626655.1	1530042	1530042	type	True	80.6109	1257	2913	95	below_threshold
Salinispora vitiensis	strain=DSM 45548	GCA_000378825.1	999544	999544	type	True	79.8642	787	2913	95	below_threshold
Salinispora vitiensis	strain=CNT-148	GCA_000514675.1	999544	999544	type	True	79.8085	792	2913	95	below_threshold
Salinispora arenicola	strain=DSM 44819	GCA_006716065.1	168697	168697	type	True	79.6669	815	2913	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	79.0704	1232	2913	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	78.9531	1201	2913	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	78.3001	1025	2913	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	75.9725	493	2913	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:04,340] [INFO] DFAST Taxonomy check result was written to GCF_003633685.1_ASM363368v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:04,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:04,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:04,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05a09046-f1b2-4be2-b9e9-c211bcb10a5a/dqc_reference/checkm_data
[2024-01-24 15:20:04,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:04,419] [INFO] Task started: CheckM
[2024-01-24 15:20:04,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003633685.1_ASM363368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003633685.1_ASM363368v1_genomic.fna/checkm_input GCF_003633685.1_ASM363368v1_genomic.fna/checkm_result
[2024-01-24 15:21:36,321] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:36,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:36,349] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:36,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:36,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003633685.1_ASM363368v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:36,350] [INFO] Task started: Blastn
[2024-01-24 15:21:36,350] [INFO] Running command: blastn -query GCF_003633685.1_ASM363368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05a09046-f1b2-4be2-b9e9-c211bcb10a5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003633685.1_ASM363368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:38,122] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:38,126] [INFO] Selected 25 target genomes.
[2024-01-24 15:21:38,127] [INFO] Target genome list was writen to GCF_003633685.1_ASM363368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:38,146] [INFO] Task started: fastANI
[2024-01-24 15:21:38,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg8df0b36b-9ca2-44af-8691-2f177d1792e2/GCF_003633685.1_ASM363368v1_genomic.fna.gz --refList GCF_003633685.1_ASM363368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003633685.1_ASM363368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:22:21,328] [INFO] Task succeeded: fastANI
[2024-01-24 15:22:21,353] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:22:21,354] [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_003633685.1	s__Micromonospora_G pisi	100.0	2911	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003030345.1	s__Plantactinospora sp003030345	81.6886	1479	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_016862935.1	s__Plantactinospora mayteni	81.5965	1464	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862915.1	s__Plantactinospora endophytica	81.5586	1511	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	81.538	1207	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874095.1	s__Plantactinospora soyae	81.4505	1495	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846275.1	s__Plantactinospora sp002846275	81.4192	1408	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217235.1	s__Plantactinospora sp004217235	81.4078	1298	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	81.3929	1261	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_900090285.1	s__Micromonospora inositola	81.3866	1189	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598485.1	s__Micromonospora veneta	81.3276	1168	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015690345.1	s__Plantactinospora sp015690345	81.2426	1336	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	81.2345	1238	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667505.1	s__Micromonospora sp003667505	81.1768	1165	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_900090305.1	s__Micromonospora siamensis	81.061	1173	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017614955.1	s__Micromonospora echinofusca_A	81.0095	1087	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908295.1	s__Micromonospora rubida	80.9345	1210	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	80.9178	1273	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_900091425.1	s__Micromonospora krabiensis	80.9012	1281	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236315.1	s__Micromonospora craterilacus	80.8264	1109	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091615.1	s__Micromonospora yangpuensis	80.7977	1150	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900090105.1	s__Micromonospora humi	80.7308	1221	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003027925.1	s__Micromonospora sp003027925	80.6722	1202	2913	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	80.6698	1152	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_003626655.1	s__Micromonospora costi	80.6216	1255	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:22:21,356] [INFO] GTDB search result was written to GCF_003633685.1_ASM363368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:22:21,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:22:21,362] [INFO] DFAST_QC result json was written to GCF_003633685.1_ASM363368v1_genomic.fna/dqc_result.json
[2024-01-24 15:22:21,362] [INFO] DFAST_QC completed!
[2024-01-24 15:22:21,362] [INFO] Total running time: 0h3m42s