[2024-01-25 18:01:05,619] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:01:05,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:01:05,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg7be69003-f45b-4ff1-8911-60fc5aff8bf5/dqc_reference
[2024-01-25 18:01:06,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:01:06,834] [INFO] Task started: Prodigal
[2024-01-25 18:01:06,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg49a168a0-c6c3-4b12-bd63-ce16ba22ddd9/GCF_030811575.1_ASM3081157v1_genomic.fna.gz | prodigal -d GCF_030811575.1_ASM3081157v1_genomic.fna/cds.fna -a GCF_030811575.1_ASM3081157v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:41,704] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:41,705] [INFO] Task started: HMMsearch
[2024-01-25 18:01:41,705] [INFO] Running command: hmmsearch --tblout GCF_030811575.1_ASM3081157v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7be69003-f45b-4ff1-8911-60fc5aff8bf5/dqc_reference/reference_markers.hmm GCF_030811575.1_ASM3081157v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:42,156] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:42,157] [INFO] Found 6/6 markers.
[2024-01-25 18:01:42,225] [INFO] Query marker FASTA was written to GCF_030811575.1_ASM3081157v1_genomic.fna/markers.fasta
[2024-01-25 18:01:42,226] [INFO] Task started: Blastn
[2024-01-25 18:01:42,226] [INFO] Running command: blastn -query GCF_030811575.1_ASM3081157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7be69003-f45b-4ff1-8911-60fc5aff8bf5/dqc_reference/reference_markers.fasta -out GCF_030811575.1_ASM3081157v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:43,443] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:43,447] [INFO] Selected 31 target genomes.
[2024-01-25 18:01:43,447] [INFO] Target genome list was writen to GCF_030811575.1_ASM3081157v1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:43,460] [INFO] Task started: fastANI
[2024-01-25 18:01:43,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg49a168a0-c6c3-4b12-bd63-ce16ba22ddd9/GCF_030811575.1_ASM3081157v1_genomic.fna.gz --refList GCF_030811575.1_ASM3081157v1_genomic.fna/target_genomes.txt --output GCF_030811575.1_ASM3081157v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:42,514] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:42,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7be69003-f45b-4ff1-8911-60fc5aff8bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:42,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7be69003-f45b-4ff1-8911-60fc5aff8bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:42,532] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:02:42,532] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:02:42,532] [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 aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	79.2615	1180	3218	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	79.2026	1004	3218	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	79.1873	1138	3218	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.1706	1200	3218	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	79.1674	1110	3218	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.1026	1014	3218	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	79.0613	1180	3218	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	79.059	1160	3218	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	79.0454	1127	3218	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	78.9759	1170	3218	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	78.9437	1106	3218	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	78.8865	1132	3218	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	78.8787	1174	3218	95	below_threshold
Actinoplanes missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	78.7389	1327	3218	95	below_threshold
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	78.6797	1083	3218	95	below_threshold
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	78.6548	1259	3218	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	78.5851	1287	3218	95	below_threshold
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	78.5664	1237	3218	95	below_threshold
Actinoplanes regularis	strain=NBRC 12514	GCA_016862355.1	52697	52697	type	True	78.5642	1238	3218	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	78.5318	1169	3218	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	78.5213	1373	3218	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	78.5172	1329	3218	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	78.4541	1337	3218	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	78.4526	1319	3218	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	78.3301	1381	3218	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	78.3277	1365	3218	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	78.2924	1201	3218	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.6595	1005	3218	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.5927	1372	3218	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.5042	1181	3218	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.3436	1263	3218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:42,534] [INFO] DFAST Taxonomy check result was written to GCF_030811575.1_ASM3081157v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:42,534] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:42,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:42,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7be69003-f45b-4ff1-8911-60fc5aff8bf5/dqc_reference/checkm_data
[2024-01-25 18:02:42,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:42,622] [INFO] Task started: CheckM
[2024-01-25 18:02:42,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030811575.1_ASM3081157v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030811575.1_ASM3081157v1_genomic.fna/checkm_input GCF_030811575.1_ASM3081157v1_genomic.fna/checkm_result
[2024-01-25 18:05:01,372] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:01,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:01,426] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:01,426] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:01,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030811575.1_ASM3081157v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:01,427] [INFO] Task started: Blastn
[2024-01-25 18:05:01,428] [INFO] Running command: blastn -query GCF_030811575.1_ASM3081157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7be69003-f45b-4ff1-8911-60fc5aff8bf5/dqc_reference/reference_markers_gtdb.fasta -out GCF_030811575.1_ASM3081157v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:03,358] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:03,361] [INFO] Selected 28 target genomes.
[2024-01-25 18:05:03,362] [INFO] Target genome list was writen to GCF_030811575.1_ASM3081157v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:03,379] [INFO] Task started: fastANI
[2024-01-25 18:05:03,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg49a168a0-c6c3-4b12-bd63-ce16ba22ddd9/GCF_030811575.1_ASM3081157v1_genomic.fna.gz --refList GCF_030811575.1_ASM3081157v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030811575.1_ASM3081157v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:02,256] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:02,272] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:06:02,273] [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_000717135.1	s__Catenuloplanes japonicus	86.6601	2261	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catenuloplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000145235.1	s__Micromonospora aurantiaca	79.2281	1187	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	98.37	95.58	0.90	0.84	15	-
GCF_900091605.1	s__Micromonospora tulbaghiae	79.227	1124	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	79.2186	1000	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	79.1746	1054	3218	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	79.1577	1145	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_013694245.1	s__Micromonospora sp013694245	79.095	1221	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	79.0388	1167	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_004217615.1	s__Micromonospora kangleipakensis	79.0276	1136	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000982955.1	s__Micromonospora sp000982955	78.9888	1117	3218	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	78.9613	1171	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090315.1	s__Micromonospora citrea	78.9417	1157	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091555.1	s__Micromonospora mirobrigensis	78.9151	1112	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091425.1	s__Micromonospora krabiensis	78.8837	1128	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	78.8347	1200	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284295.1	s__Actinoplanes missouriensis	78.7431	1320	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001265.1	s__Actinoplanes sp004001265	78.6276	1283	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	78.5782	1157	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_900188005.1	s__Actinoplanes regularis	78.5717	1236	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014203835.1	s__Micromonospora_H polyrhachis	78.5626	829	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	78.5339	1078	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	78.5262	1327	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633685.1	s__Micromonospora_G pisi	78.4529	1059	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188485.1	s__Asanoa hainanensis	78.3272	1193	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	78.2597	1382	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716715.1	s__Dactylosporangium aurantiacum	77.5062	1373	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647515.1	s__Dactylosporangium sucinum	77.4647	1338	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	77.3149	1373	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:02,274] [INFO] GTDB search result was written to GCF_030811575.1_ASM3081157v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:02,275] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:02,279] [INFO] DFAST_QC result json was written to GCF_030811575.1_ASM3081157v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:02,279] [INFO] DFAST_QC completed!
[2024-01-25 18:06:02,279] [INFO] Total running time: 0h4m57s