[2024-01-24 13:36:41,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:41,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:41,890] [INFO] DQC Reference Directory: /var/lib/cwl/stge53e004d-6c13-48da-aefb-40d85ce470c8/dqc_reference
[2024-01-24 13:36:43,138] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:43,139] [INFO] Task started: Prodigal
[2024-01-24 13:36:43,139] [INFO] Running command: gunzip -c /var/lib/cwl/stg50b7385d-f6ea-41b0-b66b-34638f09f4ee/GCF_014680085.1_ASM1468008v1_genomic.fna.gz | prodigal -d GCF_014680085.1_ASM1468008v1_genomic.fna/cds.fna -a GCF_014680085.1_ASM1468008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:07,261] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:07,262] [INFO] Task started: HMMsearch
[2024-01-24 13:37:07,262] [INFO] Running command: hmmsearch --tblout GCF_014680085.1_ASM1468008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge53e004d-6c13-48da-aefb-40d85ce470c8/dqc_reference/reference_markers.hmm GCF_014680085.1_ASM1468008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:07,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:07,716] [INFO] Found 6/6 markers.
[2024-01-24 13:37:07,784] [INFO] Query marker FASTA was written to GCF_014680085.1_ASM1468008v1_genomic.fna/markers.fasta
[2024-01-24 13:37:07,784] [INFO] Task started: Blastn
[2024-01-24 13:37:07,784] [INFO] Running command: blastn -query GCF_014680085.1_ASM1468008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge53e004d-6c13-48da-aefb-40d85ce470c8/dqc_reference/reference_markers.fasta -out GCF_014680085.1_ASM1468008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:08,962] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:08,966] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:08,967] [INFO] Target genome list was writen to GCF_014680085.1_ASM1468008v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:08,978] [INFO] Task started: fastANI
[2024-01-24 13:37:08,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b7385d-f6ea-41b0-b66b-34638f09f4ee/GCF_014680085.1_ASM1468008v1_genomic.fna.gz --refList GCF_014680085.1_ASM1468008v1_genomic.fna/target_genomes.txt --output GCF_014680085.1_ASM1468008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:48,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:48,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge53e004d-6c13-48da-aefb-40d85ce470c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:48,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge53e004d-6c13-48da-aefb-40d85ce470c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:48,720] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:48,720] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:37:48,721] [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 sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	100.0	2308	2310	95	inconclusive
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	99.9976	2304	2310	95	inconclusive
Micromonospora inyonensis	strain=DSM 46123	GCA_900091415.1	47866	47866	type	True	96.1517	1714	2310	95	inconclusive
Micromonospora echinospora	strain=DSM 43816	GCA_900091495.1	1877	1877	type	True	91.8906	1944	2310	95	below_threshold
Micromonospora echinospora	strain=ATCC 15837	GCA_002266845.1	1877	1877	type	True	91.8237	1920	2310	95	below_threshold
Micromonospora pallida	strain=DSM 43817	GCA_900090325.1	145854	145854	type	True	90.3608	1835	2310	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.5668	1072	2310	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	84.2411	1420	2310	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	84.0423	1313	2310	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	83.9254	1294	2310	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.9057	1364	2310	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.8675	1175	2310	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	83.8008	1373	2310	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.7369	1394	2310	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	83.6764	1328	2310	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.224	1183	2310	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	82.9638	1185	2310	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	82.9509	1185	2310	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	82.8902	1238	2310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:48,728] [INFO] DFAST Taxonomy check result was written to GCF_014680085.1_ASM1468008v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:48,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:48,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:48,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge53e004d-6c13-48da-aefb-40d85ce470c8/dqc_reference/checkm_data
[2024-01-24 13:37:48,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:48,795] [INFO] Task started: CheckM
[2024-01-24 13:37:48,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014680085.1_ASM1468008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014680085.1_ASM1468008v1_genomic.fna/checkm_input GCF_014680085.1_ASM1468008v1_genomic.fna/checkm_result
[2024-01-24 13:39:33,647] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:33,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:33,671] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:33,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:33,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014680085.1_ASM1468008v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:33,672] [INFO] Task started: Blastn
[2024-01-24 13:39:33,672] [INFO] Running command: blastn -query GCF_014680085.1_ASM1468008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge53e004d-6c13-48da-aefb-40d85ce470c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014680085.1_ASM1468008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:35,413] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:35,417] [INFO] Selected 24 target genomes.
[2024-01-24 13:39:35,417] [INFO] Target genome list was writen to GCF_014680085.1_ASM1468008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:35,516] [INFO] Task started: fastANI
[2024-01-24 13:39:35,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b7385d-f6ea-41b0-b66b-34638f09f4ee/GCF_014680085.1_ASM1468008v1_genomic.fna.gz --refList GCF_014680085.1_ASM1468008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014680085.1_ASM1468008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:18,774] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:18,797] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:18,798] [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_900091415.1	s__Micromonospora inyonensis	96.1157	1717	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.10	96.06	0.74	0.74	3	conclusive
GCF_900091495.1	s__Micromonospora echinospora	91.8942	1943	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.77	97.55	0.96	0.91	3	-
GCF_900090325.1	s__Micromonospora pallida	90.3327	1840	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	84.7345	1436	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	84.572	1373	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	84.5582	1393	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_018070575.1	s__Micromonospora sp018070575	84.465	1403	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	84.4373	1313	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830265.1	s__Micromonospora olivasterospora	84.2893	1294	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016802835.1	s__Micromonospora sp016802835	84.2609	965	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	84.2225	1454	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_900091625.1	s__Micromonospora peucetia	84.2014	1425	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	84.1865	1247	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567585.1	s__Micromonospora rosaria	84.1341	1300	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725545.1	s__Micromonospora sp003725545	84.1098	1200	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_008868175.1	s__Micromonospora sp008868175	84.0127	1227	2310	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	83.7475	1235	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_900091475.1	s__Micromonospora chersina	83.7331	1381	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_900091455.1	s__Micromonospora coriariae	83.7048	1309	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090105.1	s__Micromonospora humi	83.6257	1334	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364215.1	s__Micromonospora sp004307965	83.0939	1248	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_010560025.1	s__Micromonospora sp010560025	82.9969	1212	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_014764405.1	s__Micromonospora craniellae	82.9686	1183	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_016863495.1	s__Micromonospora andamanensis	82.5426	1223	2310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:18,801] [INFO] GTDB search result was written to GCF_014680085.1_ASM1468008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:18,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:18,806] [INFO] DFAST_QC result json was written to GCF_014680085.1_ASM1468008v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:18,806] [INFO] DFAST_QC completed!
[2024-01-24 13:40:18,806] [INFO] Total running time: 0h3m37s