[2024-01-24 13:18:26,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,428] [INFO] DQC Reference Directory: /var/lib/cwl/stge96edcd2-de10-40d2-8904-8df2ae66c19a/dqc_reference
[2024-01-24 13:18:27,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,547] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,548] [INFO] Running command: gunzip -c /var/lib/cwl/stgc622d52d-8d31-4d0d-872e-1e78778d18b9/GCF_020884795.1_ASM2088479v1_genomic.fna.gz | prodigal -d GCF_020884795.1_ASM2088479v1_genomic.fna/cds.fna -a GCF_020884795.1_ASM2088479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:45,738] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:45,738] [INFO] Task started: HMMsearch
[2024-01-24 13:18:45,738] [INFO] Running command: hmmsearch --tblout GCF_020884795.1_ASM2088479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge96edcd2-de10-40d2-8904-8df2ae66c19a/dqc_reference/reference_markers.hmm GCF_020884795.1_ASM2088479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:46,050] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:46,055] [INFO] Found 6/6 markers.
[2024-01-24 13:18:46,117] [INFO] Query marker FASTA was written to GCF_020884795.1_ASM2088479v1_genomic.fna/markers.fasta
[2024-01-24 13:18:46,117] [INFO] Task started: Blastn
[2024-01-24 13:18:46,117] [INFO] Running command: blastn -query GCF_020884795.1_ASM2088479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge96edcd2-de10-40d2-8904-8df2ae66c19a/dqc_reference/reference_markers.fasta -out GCF_020884795.1_ASM2088479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:47,369] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:47,372] [INFO] Selected 22 target genomes.
[2024-01-24 13:18:47,373] [INFO] Target genome list was writen to GCF_020884795.1_ASM2088479v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:47,387] [INFO] Task started: fastANI
[2024-01-24 13:18:47,387] [INFO] Running command: fastANI --query /var/lib/cwl/stgc622d52d-8d31-4d0d-872e-1e78778d18b9/GCF_020884795.1_ASM2088479v1_genomic.fna.gz --refList GCF_020884795.1_ASM2088479v1_genomic.fna/target_genomes.txt --output GCF_020884795.1_ASM2088479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:32,970] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:32,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge96edcd2-de10-40d2-8904-8df2ae66c19a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:32,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge96edcd2-de10-40d2-8904-8df2ae66c19a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:32,988] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:32,989] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:32,989] [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 rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	88.6831	1545	2130	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	88.6414	1518	2130	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	88.5704	1531	2130	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	88.5654	1537	2130	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	88.5572	1551	2130	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	86.9761	1328	2130	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	85.7177	1369	2130	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.4487	1018	2130	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	85.2625	1421	2130	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	85.1875	1222	2130	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	85.1068	1340	2130	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.9821	1377	2130	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.9641	1355	2130	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.7851	1170	2130	95	below_threshold
Micromonospora coriariae	strain=DSM 44875	GCA_900091455.1	285665	285665	type	True	84.4848	1307	2130	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	84.4017	1359	2130	95	below_threshold
Micromonospora sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	84.3563	1372	2130	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	84.3053	1298	2130	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	83.3335	1215	2130	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	83.3317	1209	2130	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	83.3184	1217	2130	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.4666	621	2130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:32,990] [INFO] DFAST Taxonomy check result was written to GCF_020884795.1_ASM2088479v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:32,991] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:32,991] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:32,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge96edcd2-de10-40d2-8904-8df2ae66c19a/dqc_reference/checkm_data
[2024-01-24 13:19:32,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:33,052] [INFO] Task started: CheckM
[2024-01-24 13:19:33,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020884795.1_ASM2088479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020884795.1_ASM2088479v1_genomic.fna/checkm_input GCF_020884795.1_ASM2088479v1_genomic.fna/checkm_result
[2024-01-24 13:20:32,794] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:32,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:32,813] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:32,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:32,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020884795.1_ASM2088479v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:32,814] [INFO] Task started: Blastn
[2024-01-24 13:20:32,814] [INFO] Running command: blastn -query GCF_020884795.1_ASM2088479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge96edcd2-de10-40d2-8904-8df2ae66c19a/dqc_reference/reference_markers_gtdb.fasta -out GCF_020884795.1_ASM2088479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:34,516] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:34,520] [INFO] Selected 20 target genomes.
[2024-01-24 13:20:34,520] [INFO] Target genome list was writen to GCF_020884795.1_ASM2088479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:34,539] [INFO] Task started: fastANI
[2024-01-24 13:20:34,540] [INFO] Running command: fastANI --query /var/lib/cwl/stgc622d52d-8d31-4d0d-872e-1e78778d18b9/GCF_020884795.1_ASM2088479v1_genomic.fna.gz --refList GCF_020884795.1_ASM2088479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020884795.1_ASM2088479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:13,194] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:13,209] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:21:13,209] [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_003434305.1	s__Micromonospora sp003434305	89.0307	1486	2130	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	88.6575	1547	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	88.657	1516	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_014205165.1	s__Micromonospora carbonacea	88.5861	1535	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_000158815.1	s__Micromonospora sp000158815	88.2606	1353	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.02	97.02	0.80	0.80	2	-
GCF_007830265.1	s__Micromonospora olivasterospora	86.9528	1330	2130	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	85.7862	1361	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089595.1	s__Micromonospora auratinigra	85.3437	1358	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091625.1	s__Micromonospora peucetia	85.3249	1414	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070575.1	s__Micromonospora sp018070575	85.3168	1367	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725545.1	s__Micromonospora sp003725545	85.2417	1196	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_900091555.1	s__Micromonospora mirobrigensis	85.2284	1282	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	85.2199	1218	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	85.087	1342	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_003667505.1	s__Micromonospora sp003667505	84.6693	1223	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_002926165.1	s__Micromonospora chalcea	84.6593	1341	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_900091565.1	s__Micromonospora marina	84.6503	1306	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.96	0.90	0.86	3	-
GCF_900091455.1	s__Micromonospora coriariae	84.4871	1306	2130	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	83.2885	1162	2130	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	83.0046	1183	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:13,211] [INFO] GTDB search result was written to GCF_020884795.1_ASM2088479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:13,212] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:13,218] [INFO] DFAST_QC result json was written to GCF_020884795.1_ASM2088479v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:13,219] [INFO] DFAST_QC completed!
[2024-01-24 13:21:13,219] [INFO] Total running time: 0h2m47s