[2024-01-25 19:38:35,637] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:35,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:35,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f5e968e-699d-4bd4-abb6-5daf817e2d30/dqc_reference
[2024-01-25 19:38:36,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:36,829] [INFO] Task started: Prodigal
[2024-01-25 19:38:36,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ff68666-93d6-4bbc-b321-b1f09d037c76/GCF_016901255.1_ASM1690125v1_genomic.fna.gz | prodigal -d GCF_016901255.1_ASM1690125v1_genomic.fna/cds.fna -a GCF_016901255.1_ASM1690125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:01,373] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:01,374] [INFO] Task started: HMMsearch
[2024-01-25 19:39:01,374] [INFO] Running command: hmmsearch --tblout GCF_016901255.1_ASM1690125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f5e968e-699d-4bd4-abb6-5daf817e2d30/dqc_reference/reference_markers.hmm GCF_016901255.1_ASM1690125v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:01,716] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:01,717] [INFO] Found 6/6 markers.
[2024-01-25 19:39:01,771] [INFO] Query marker FASTA was written to GCF_016901255.1_ASM1690125v1_genomic.fna/markers.fasta
[2024-01-25 19:39:01,772] [INFO] Task started: Blastn
[2024-01-25 19:39:01,772] [INFO] Running command: blastn -query GCF_016901255.1_ASM1690125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f5e968e-699d-4bd4-abb6-5daf817e2d30/dqc_reference/reference_markers.fasta -out GCF_016901255.1_ASM1690125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:02,929] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:02,932] [INFO] Selected 11 target genomes.
[2024-01-25 19:39:02,933] [INFO] Target genome list was writen to GCF_016901255.1_ASM1690125v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:02,938] [INFO] Task started: fastANI
[2024-01-25 19:39:02,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ff68666-93d6-4bbc-b321-b1f09d037c76/GCF_016901255.1_ASM1690125v1_genomic.fna.gz --refList GCF_016901255.1_ASM1690125v1_genomic.fna/target_genomes.txt --output GCF_016901255.1_ASM1690125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:27,184] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:27,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f5e968e-699d-4bd4-abb6-5daf817e2d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:27,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f5e968e-699d-4bd4-abb6-5daf817e2d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:27,193] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:39:27,193] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:39:27,194] [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 humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	100.0	2428	2430	95	inconclusive
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	96.0117	2056	2430	95	inconclusive
Micromonospora matsumotoense	strain=DSM 44100	GCA_900091525.1	121616	121616	type	True	92.1667	2008	2430	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	91.6595	1938	2430	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	91.5817	1746	2430	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	86.4867	1428	2430	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	85.8358	1655	2430	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.0028	1059	2430	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.8915	1505	2430	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.4751	1256	2430	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.3115	1321	2430	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:27,195] [INFO] DFAST Taxonomy check result was written to GCF_016901255.1_ASM1690125v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:27,195] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:27,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:27,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f5e968e-699d-4bd4-abb6-5daf817e2d30/dqc_reference/checkm_data
[2024-01-25 19:39:27,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:27,263] [INFO] Task started: CheckM
[2024-01-25 19:39:27,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016901255.1_ASM1690125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016901255.1_ASM1690125v1_genomic.fna/checkm_input GCF_016901255.1_ASM1690125v1_genomic.fna/checkm_result
[2024-01-25 19:41:10,390] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:10,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:10,412] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:10,412] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:10,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016901255.1_ASM1690125v1_genomic.fna/markers.fasta)
[2024-01-25 19:41:10,415] [INFO] Task started: Blastn
[2024-01-25 19:41:10,415] [INFO] Running command: blastn -query GCF_016901255.1_ASM1690125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f5e968e-699d-4bd4-abb6-5daf817e2d30/dqc_reference/reference_markers_gtdb.fasta -out GCF_016901255.1_ASM1690125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:12,211] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:12,214] [INFO] Selected 11 target genomes.
[2024-01-25 19:41:12,214] [INFO] Target genome list was writen to GCF_016901255.1_ASM1690125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:12,220] [INFO] Task started: fastANI
[2024-01-25 19:41:12,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ff68666-93d6-4bbc-b321-b1f09d037c76/GCF_016901255.1_ASM1690125v1_genomic.fna.gz --refList GCF_016901255.1_ASM1690125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016901255.1_ASM1690125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:37,275] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:37,283] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:37,283] [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_002210435.1	s__Micromonospora wenchangensis	95.9981	2057	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	conclusive
GCF_017599305.1	s__Micromonospora sp017599305	93.1479	2074	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091525.1	s__Micromonospora matsumotoense	92.1393	2011	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090265.1	s__Micromonospora rifamycinica	91.635	1941	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900090245.1	s__Micromonospora halophytica	86.534	1422	2430	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	86.41	1528	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	86.3596	1447	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_014205165.1	s__Micromonospora carbonacea	85.8022	1671	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_900091595.1	s__Micromonospora haikouensis	85.7946	1662	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_003434305.1	s__Micromonospora sp003434305	85.4267	1421	2430	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	84.5646	1423	2430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:37,284] [INFO] GTDB search result was written to GCF_016901255.1_ASM1690125v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:37,287] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:37,292] [INFO] DFAST_QC result json was written to GCF_016901255.1_ASM1690125v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:37,292] [INFO] DFAST_QC completed!
[2024-01-25 19:41:37,293] [INFO] Total running time: 0h3m2s