[2024-01-24 12:14:48,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ef8036d-6214-49be-8a6e-d792361629b9/dqc_reference
[2024-01-24 12:14:49,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:49,723] [INFO] Task started: Prodigal
[2024-01-24 12:14:49,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgd84460f3-ece3-4ffa-aaea-0cf878c974f6/GCF_016863575.1_ASM1686357v1_genomic.fna.gz | prodigal -d GCF_016863575.1_ASM1686357v1_genomic.fna/cds.fna -a GCF_016863575.1_ASM1686357v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:08,212] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:08,213] [INFO] Task started: HMMsearch
[2024-01-24 12:15:08,213] [INFO] Running command: hmmsearch --tblout GCF_016863575.1_ASM1686357v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ef8036d-6214-49be-8a6e-d792361629b9/dqc_reference/reference_markers.hmm GCF_016863575.1_ASM1686357v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:08,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:08,534] [INFO] Found 6/6 markers.
[2024-01-24 12:15:08,592] [INFO] Query marker FASTA was written to GCF_016863575.1_ASM1686357v1_genomic.fna/markers.fasta
[2024-01-24 12:15:08,593] [INFO] Task started: Blastn
[2024-01-24 12:15:08,593] [INFO] Running command: blastn -query GCF_016863575.1_ASM1686357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ef8036d-6214-49be-8a6e-d792361629b9/dqc_reference/reference_markers.fasta -out GCF_016863575.1_ASM1686357v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:09,689] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:09,693] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:09,693] [INFO] Target genome list was writen to GCF_016863575.1_ASM1686357v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:09,698] [INFO] Task started: fastANI
[2024-01-24 12:15:09,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84460f3-ece3-4ffa-aaea-0cf878c974f6/GCF_016863575.1_ASM1686357v1_genomic.fna.gz --refList GCF_016863575.1_ASM1686357v1_genomic.fna/target_genomes.txt --output GCF_016863575.1_ASM1686357v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:35,438] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:35,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ef8036d-6214-49be-8a6e-d792361629b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:35,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ef8036d-6214-49be-8a6e-d792361629b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:35,456] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:35,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:35,456] [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 phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	88.119	1560	2088	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	88.1086	1596	2088	95	below_threshold
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	88.1036	1499	2088	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	87.0831	1334	2088	95	below_threshold
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	86.4482	1420	2088	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	86.4191	1374	2088	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	86.2296	1321	2088	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	86.1522	1335	2088	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	86.0513	1449	2088	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	85.9608	1457	2088	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	85.9477	1460	2088	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	85.9175	1448	2088	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.1072	994	2088	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.3332	1161	2088	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.1664	1249	2088	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.143	1297	2088	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	83.131	1295	2088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:35,461] [INFO] DFAST Taxonomy check result was written to GCF_016863575.1_ASM1686357v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:35,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:35,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:35,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ef8036d-6214-49be-8a6e-d792361629b9/dqc_reference/checkm_data
[2024-01-24 12:15:35,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:35,523] [INFO] Task started: CheckM
[2024-01-24 12:15:35,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863575.1_ASM1686357v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863575.1_ASM1686357v1_genomic.fna/checkm_input GCF_016863575.1_ASM1686357v1_genomic.fna/checkm_result
[2024-01-24 12:16:34,289] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:34,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:34,316] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:34,316] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:34,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863575.1_ASM1686357v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:34,317] [INFO] Task started: Blastn
[2024-01-24 12:16:34,317] [INFO] Running command: blastn -query GCF_016863575.1_ASM1686357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ef8036d-6214-49be-8a6e-d792361629b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863575.1_ASM1686357v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:36,020] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:36,026] [INFO] Selected 13 target genomes.
[2024-01-24 12:16:36,026] [INFO] Target genome list was writen to GCF_016863575.1_ASM1686357v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:36,036] [INFO] Task started: fastANI
[2024-01-24 12:16:36,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84460f3-ece3-4ffa-aaea-0cf878c974f6/GCF_016863575.1_ASM1686357v1_genomic.fna.gz --refList GCF_016863575.1_ASM1686357v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863575.1_ASM1686357v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:57,368] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:57,379] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:57,380] [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_900112325.1	s__Micromonospora sediminimaris	99.9986	2085	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.06	96.13	0.95	0.90	3	conclusive
GCF_018070465.1	s__Micromonospora sp018070465	92.5053	1657	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010560025.1	s__Micromonospora sp010560025	92.4776	1670	2088	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	91.5842	1689	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_016863535.1	s__Micromonospora lutea	90.4663	1565	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712475.1	s__Micromonospora sp009712475	89.88	1528	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646235.1	s__Micromonospora sonchi	86.5167	1410	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331455.1	s__Micromonospora zingiberis	86.4625	1418	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863555.1	s__Micromonospora qiuiae	86.433	1405	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764405.1	s__Micromonospora craniellae	86.1686	1332	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_004345505.1	s__Micromonospora sp004345505	83.9979	1306	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.85	96.85	0.87	0.87	2	-
GCF_900091625.1	s__Micromonospora peucetia	83.6558	1281	2088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707425.1	s__Micromonospora sp009707425	83.426	1256	2088	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 12:16:57,382] [INFO] GTDB search result was written to GCF_016863575.1_ASM1686357v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:57,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:57,387] [INFO] DFAST_QC result json was written to GCF_016863575.1_ASM1686357v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:57,387] [INFO] DFAST_QC completed!
[2024-01-24 12:16:57,387] [INFO] Total running time: 0h2m9s