[2024-01-24 14:22:04,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,675] [INFO] DQC Reference Directory: /var/lib/cwl/stge1ec45f5-0173-4d77-89f0-37538e586029/dqc_reference
[2024-01-24 14:22:05,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,985] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,985] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4f15ec4-5910-4ad8-a0e5-6f8a14609f2b/GCF_014205165.1_ASM1420516v1_genomic.fna.gz | prodigal -d GCF_014205165.1_ASM1420516v1_genomic.fna/cds.fna -a GCF_014205165.1_ASM1420516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:46,625] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:46,626] [INFO] Task started: HMMsearch
[2024-01-24 14:22:46,626] [INFO] Running command: hmmsearch --tblout GCF_014205165.1_ASM1420516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1ec45f5-0173-4d77-89f0-37538e586029/dqc_reference/reference_markers.hmm GCF_014205165.1_ASM1420516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:46,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:46,975] [INFO] Found 6/6 markers.
[2024-01-24 14:22:47,034] [INFO] Query marker FASTA was written to GCF_014205165.1_ASM1420516v1_genomic.fna/markers.fasta
[2024-01-24 14:22:47,034] [INFO] Task started: Blastn
[2024-01-24 14:22:47,034] [INFO] Running command: blastn -query GCF_014205165.1_ASM1420516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1ec45f5-0173-4d77-89f0-37538e586029/dqc_reference/reference_markers.fasta -out GCF_014205165.1_ASM1420516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:48,327] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:48,330] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:48,330] [INFO] Target genome list was writen to GCF_014205165.1_ASM1420516v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:48,339] [INFO] Task started: fastANI
[2024-01-24 14:22:48,339] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4f15ec4-5910-4ad8-a0e5-6f8a14609f2b/GCF_014205165.1_ASM1420516v1_genomic.fna.gz --refList GCF_014205165.1_ASM1420516v1_genomic.fna/target_genomes.txt --output GCF_014205165.1_ASM1420516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:23,722] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:23,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1ec45f5-0173-4d77-89f0-37538e586029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:23,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1ec45f5-0173-4d77-89f0-37538e586029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:23,739] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:23:23,739] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:23:23,739] [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 carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	100.0	2506	2509	95	inconclusive
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	99.9983	2507	2509	95	inconclusive
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	98.3766	2280	2509	95	inconclusive
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	95.5348	2045	2509	95	inconclusive
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	88.1883	1665	2509	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	87.0236	1425	2509	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	85.9348	1462	2509	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.8015	1652	2509	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.4178	1092	2509	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	85.2887	1468	2509	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	85.0347	1550	2509	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	84.8501	1426	2509	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.6169	1299	2509	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	83.5477	1334	2509	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.5398	1328	2509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:23,741] [INFO] DFAST Taxonomy check result was written to GCF_014205165.1_ASM1420516v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:23,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:23,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:23,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1ec45f5-0173-4d77-89f0-37538e586029/dqc_reference/checkm_data
[2024-01-24 14:23:23,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:23,810] [INFO] Task started: CheckM
[2024-01-24 14:23:23,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205165.1_ASM1420516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205165.1_ASM1420516v1_genomic.fna/checkm_input GCF_014205165.1_ASM1420516v1_genomic.fna/checkm_result
[2024-01-24 14:25:58,975] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:58,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:58,997] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:58,998] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:58,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205165.1_ASM1420516v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:58,999] [INFO] Task started: Blastn
[2024-01-24 14:25:58,999] [INFO] Running command: blastn -query GCF_014205165.1_ASM1420516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1ec45f5-0173-4d77-89f0-37538e586029/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205165.1_ASM1420516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:26:01,276] [INFO] Task succeeded: Blastn
[2024-01-24 14:26:01,280] [INFO] Selected 12 target genomes.
[2024-01-24 14:26:01,281] [INFO] Target genome list was writen to GCF_014205165.1_ASM1420516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:26:01,391] [INFO] Task started: fastANI
[2024-01-24 14:26:01,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4f15ec4-5910-4ad8-a0e5-6f8a14609f2b/GCF_014205165.1_ASM1420516v1_genomic.fna.gz --refList GCF_014205165.1_ASM1420516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205165.1_ASM1420516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:33,328] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:33,340] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:26:33,341] [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_014205165.1	s__Micromonospora carbonacea	100.0	2507	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	inconclusive
GCF_900091595.1	s__Micromonospora haikouensis	95.5555	2043	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	inconclusive
GCF_000158815.1	s__Micromonospora sp000158815	91.6448	1702	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.02	97.02	0.80	0.80	2	-
GCF_003434305.1	s__Micromonospora sp003434305	88.7768	1651	2509	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	88.1662	1667	2509	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	86.9791	1432	2509	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	85.9835	1455	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664255.1	s__Micromonospora sp003664255	85.3654	1552	2509	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	85.1968	1481	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_900089605.1	s__Micromonospora narathiwatensis	84.9247	1416	2509	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	84.7964	1471	2509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_900090225.1	s__Micromonospora eburnea	84.5438	1403	2509	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 14:26:33,343] [INFO] GTDB search result was written to GCF_014205165.1_ASM1420516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:33,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:33,352] [INFO] DFAST_QC result json was written to GCF_014205165.1_ASM1420516v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:33,352] [INFO] DFAST_QC completed!
[2024-01-24 14:26:33,353] [INFO] Total running time: 0h4m29s