[2024-01-24 13:22:40,765] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:40,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:40,767] [INFO] DQC Reference Directory: /var/lib/cwl/stge222dd5b-b11f-4763-88c3-b25b421ed90a/dqc_reference
[2024-01-24 13:22:42,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:42,096] [INFO] Task started: Prodigal
[2024-01-24 13:22:42,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg891094a1-fe4f-42e5-8af3-35fb97490477/GCF_002210435.1_ASM221043v1_genomic.fna.gz | prodigal -d GCF_002210435.1_ASM221043v1_genomic.fna/cds.fna -a GCF_002210435.1_ASM221043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:03,286] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:03,287] [INFO] Task started: HMMsearch
[2024-01-24 13:23:03,287] [INFO] Running command: hmmsearch --tblout GCF_002210435.1_ASM221043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge222dd5b-b11f-4763-88c3-b25b421ed90a/dqc_reference/reference_markers.hmm GCF_002210435.1_ASM221043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:03,646] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:03,648] [INFO] Found 6/6 markers.
[2024-01-24 13:23:03,705] [INFO] Query marker FASTA was written to GCF_002210435.1_ASM221043v1_genomic.fna/markers.fasta
[2024-01-24 13:23:03,705] [INFO] Task started: Blastn
[2024-01-24 13:23:03,706] [INFO] Running command: blastn -query GCF_002210435.1_ASM221043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge222dd5b-b11f-4763-88c3-b25b421ed90a/dqc_reference/reference_markers.fasta -out GCF_002210435.1_ASM221043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:04,988] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:04,992] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:04,993] [INFO] Target genome list was writen to GCF_002210435.1_ASM221043v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:05,010] [INFO] Task started: fastANI
[2024-01-24 13:23:05,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg891094a1-fe4f-42e5-8af3-35fb97490477/GCF_002210435.1_ASM221043v1_genomic.fna.gz --refList GCF_002210435.1_ASM221043v1_genomic.fna/target_genomes.txt --output GCF_002210435.1_ASM221043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:34,498] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:34,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge222dd5b-b11f-4763-88c3-b25b421ed90a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:34,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge222dd5b-b11f-4763-88c3-b25b421ed90a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:34,515] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:34,515] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:23:34,515] [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 wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	100.0	2422	2427	95	inconclusive
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	96.0092	2067	2427	95	inconclusive
Micromonospora matsumotoense	strain=DSM 44100	GCA_900091525.1	121616	121616	type	True	92.183	1928	2427	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	91.7127	1669	2427	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	91.6678	1858	2427	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	86.6809	1478	2427	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	86.0194	1648	2427	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	85.4155	1356	2427	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	85.3759	1399	2427	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	85.3442	1292	2427	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	85.0684	1451	2427	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.0437	1053	2427	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.5151	1258	2427	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.3302	1312	2427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:34,517] [INFO] DFAST Taxonomy check result was written to GCF_002210435.1_ASM221043v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:34,517] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:34,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:34,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge222dd5b-b11f-4763-88c3-b25b421ed90a/dqc_reference/checkm_data
[2024-01-24 13:23:34,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:34,584] [INFO] Task started: CheckM
[2024-01-24 13:23:34,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002210435.1_ASM221043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002210435.1_ASM221043v1_genomic.fna/checkm_input GCF_002210435.1_ASM221043v1_genomic.fna/checkm_result
[2024-01-24 13:24:50,318] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:50,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:50,344] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:50,344] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:50,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002210435.1_ASM221043v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:50,345] [INFO] Task started: Blastn
[2024-01-24 13:24:50,345] [INFO] Running command: blastn -query GCF_002210435.1_ASM221043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge222dd5b-b11f-4763-88c3-b25b421ed90a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002210435.1_ASM221043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:52,183] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:52,186] [INFO] Selected 11 target genomes.
[2024-01-24 13:24:52,187] [INFO] Target genome list was writen to GCF_002210435.1_ASM221043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:52,212] [INFO] Task started: fastANI
[2024-01-24 13:24:52,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg891094a1-fe4f-42e5-8af3-35fb97490477/GCF_002210435.1_ASM221043v1_genomic.fna.gz --refList GCF_002210435.1_ASM221043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002210435.1_ASM221043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:16,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:16,940] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:16,941] [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	100.0	2422	2427	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	92.825	2006	2427	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	92.2196	1924	2427	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	91.677	1857	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900090295.1	s__Micromonospora coxensis	86.6413	1484	2427	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	86.5952	1419	2427	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	85.9358	1669	2427	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	85.902	1643	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_004217615.1	s__Micromonospora kangleipakensis	85.3987	1358	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598485.1	s__Micromonospora veneta	85.2547	1303	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172935.1	s__Micromonospora sp003172935	85.1571	1251	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:16,943] [INFO] GTDB search result was written to GCF_002210435.1_ASM221043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:16,944] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:16,947] [INFO] DFAST_QC result json was written to GCF_002210435.1_ASM221043v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:16,947] [INFO] DFAST_QC completed!
[2024-01-24 13:25:16,947] [INFO] Total running time: 0h2m36s