[2024-01-24 13:28:13,238] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg6400ee9e-c18e-4d33-ba4c-cd2a1ed995dd/dqc_reference
[2024-01-24 13:28:14,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,541] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,541] [INFO] Running command: gunzip -c /var/lib/cwl/stgf679a48a-f2d5-43c6-8c66-7dc65e6de8b0/GCF_007829995.1_ASM782999v1_genomic.fna.gz | prodigal -d GCF_007829995.1_ASM782999v1_genomic.fna/cds.fna -a GCF_007829995.1_ASM782999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:47,768] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:47,768] [INFO] Task started: HMMsearch
[2024-01-24 13:28:47,768] [INFO] Running command: hmmsearch --tblout GCF_007829995.1_ASM782999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6400ee9e-c18e-4d33-ba4c-cd2a1ed995dd/dqc_reference/reference_markers.hmm GCF_007829995.1_ASM782999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:48,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:48,129] [INFO] Found 6/6 markers.
[2024-01-24 13:28:48,197] [INFO] Query marker FASTA was written to GCF_007829995.1_ASM782999v1_genomic.fna/markers.fasta
[2024-01-24 13:28:48,198] [INFO] Task started: Blastn
[2024-01-24 13:28:48,198] [INFO] Running command: blastn -query GCF_007829995.1_ASM782999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6400ee9e-c18e-4d33-ba4c-cd2a1ed995dd/dqc_reference/reference_markers.fasta -out GCF_007829995.1_ASM782999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:49,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:49,419] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:49,420] [INFO] Target genome list was writen to GCF_007829995.1_ASM782999v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:49,445] [INFO] Task started: fastANI
[2024-01-24 13:28:49,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgf679a48a-f2d5-43c6-8c66-7dc65e6de8b0/GCF_007829995.1_ASM782999v1_genomic.fna.gz --refList GCF_007829995.1_ASM782999v1_genomic.fna/target_genomes.txt --output GCF_007829995.1_ASM782999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:26,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:26,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6400ee9e-c18e-4d33-ba4c-cd2a1ed995dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:26,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6400ee9e-c18e-4d33-ba4c-cd2a1ed995dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:26,887] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:29:26,887] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:29:26,888] [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=DSM 43912	GCA_007829995.1	47875	47875	type	True	100.0	2308	2309	95	inconclusive
Micromonospora sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	99.9976	2306	2309	95	inconclusive
Micromonospora inyonensis	strain=DSM 46123	GCA_900091415.1	47866	47866	type	True	96.0768	1717	2309	95	inconclusive
Micromonospora echinospora	strain=ATCC 15837	GCA_002266845.1	1877	1877	type	True	91.8499	1924	2309	95	below_threshold
Micromonospora echinospora	strain=DSM 43816	GCA_900091495.1	1877	1877	type	True	91.8493	1952	2309	95	below_threshold
Micromonospora pallida	strain=DSM 43817	GCA_900090325.1	145854	145854	type	True	90.3227	1837	2309	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.7184	1065	2309	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	84.1809	1419	2309	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	84.0545	1306	2309	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	83.913	1315	2309	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.856	1377	2309	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.8417	1371	2309	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	83.8093	1382	2309	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.7871	1168	2309	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	83.664	1333	2309	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.1658	1205	2309	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	83.1096	1166	2309	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	83.0432	1193	2309	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	82.9163	1223	2309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:26,890] [INFO] DFAST Taxonomy check result was written to GCF_007829995.1_ASM782999v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:26,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:26,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:26,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6400ee9e-c18e-4d33-ba4c-cd2a1ed995dd/dqc_reference/checkm_data
[2024-01-24 13:29:26,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:26,962] [INFO] Task started: CheckM
[2024-01-24 13:29:26,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007829995.1_ASM782999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007829995.1_ASM782999v1_genomic.fna/checkm_input GCF_007829995.1_ASM782999v1_genomic.fna/checkm_result
[2024-01-24 13:31:44,109] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:44,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:44,130] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:44,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:44,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007829995.1_ASM782999v1_genomic.fna/markers.fasta)
[2024-01-24 13:31:44,132] [INFO] Task started: Blastn
[2024-01-24 13:31:44,132] [INFO] Running command: blastn -query GCF_007829995.1_ASM782999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6400ee9e-c18e-4d33-ba4c-cd2a1ed995dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_007829995.1_ASM782999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:45,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:45,943] [INFO] Selected 24 target genomes.
[2024-01-24 13:31:45,943] [INFO] Target genome list was writen to GCF_007829995.1_ASM782999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:45,965] [INFO] Task started: fastANI
[2024-01-24 13:31:45,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgf679a48a-f2d5-43c6-8c66-7dc65e6de8b0/GCF_007829995.1_ASM782999v1_genomic.fna.gz --refList GCF_007829995.1_ASM782999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007829995.1_ASM782999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:31,502] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:31,521] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:31,521] [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	96.0768	1717	2309	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	91.8674	1950	2309	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	90.3085	1842	2309	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	84.7759	1420	2309	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	84.5951	1382	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070575.1	s__Micromonospora sp018070575	84.5841	1391	2309	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	84.5502	1311	2309	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	84.5174	1415	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCA_016802835.1	s__Micromonospora sp016802835	84.4695	947	2309	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	84.3508	1290	2309	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	84.3367	1449	2309	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	84.2463	1406	2309	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	84.2412	1234	2309	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	84.2185	1201	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_001567585.1	s__Micromonospora rosaria	84.0486	1307	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	83.9588	1226	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091455.1	s__Micromonospora coriariae	83.8993	1280	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091475.1	s__Micromonospora chersina	83.8044	1382	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_003667505.1	s__Micromonospora sp003667505	83.7777	1225	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_900090105.1	s__Micromonospora humi	83.5813	1344	2309	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	83.0483	1256	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_014764405.1	s__Micromonospora craniellae	83.0277	1194	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_010560025.1	s__Micromonospora sp010560025	82.9874	1226	2309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_016863495.1	s__Micromonospora andamanensis	82.6302	1220	2309	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 13:32:31,523] [INFO] GTDB search result was written to GCF_007829995.1_ASM782999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:31,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:31,528] [INFO] DFAST_QC result json was written to GCF_007829995.1_ASM782999v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:31,529] [INFO] DFAST_QC completed!
[2024-01-24 13:32:31,529] [INFO] Total running time: 0h4m18s