[2024-01-24 14:31:00,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,267] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg75a26745-2805-445d-80e4-d7e47e8b5b9a/dqc_reference
[2024-01-24 14:31:02,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,104] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg57d89217-40f5-4bf6-8eed-6ecd17eb94e1/GCF_004331455.1_ASM433145v1_genomic.fna.gz | prodigal -d GCF_004331455.1_ASM433145v1_genomic.fna/cds.fna -a GCF_004331455.1_ASM433145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:19,674] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:19,674] [INFO] Task started: HMMsearch
[2024-01-24 14:31:19,675] [INFO] Running command: hmmsearch --tblout GCF_004331455.1_ASM433145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75a26745-2805-445d-80e4-d7e47e8b5b9a/dqc_reference/reference_markers.hmm GCF_004331455.1_ASM433145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:20,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:20,116] [INFO] Found 6/6 markers.
[2024-01-24 14:31:20,163] [INFO] Query marker FASTA was written to GCF_004331455.1_ASM433145v1_genomic.fna/markers.fasta
[2024-01-24 14:31:20,163] [INFO] Task started: Blastn
[2024-01-24 14:31:20,163] [INFO] Running command: blastn -query GCF_004331455.1_ASM433145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75a26745-2805-445d-80e4-d7e47e8b5b9a/dqc_reference/reference_markers.fasta -out GCF_004331455.1_ASM433145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:21,388] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:21,391] [INFO] Selected 15 target genomes.
[2024-01-24 14:31:21,391] [INFO] Target genome list was writen to GCF_004331455.1_ASM433145v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:21,396] [INFO] Task started: fastANI
[2024-01-24 14:31:21,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg57d89217-40f5-4bf6-8eed-6ecd17eb94e1/GCF_004331455.1_ASM433145v1_genomic.fna.gz --refList GCF_004331455.1_ASM433145v1_genomic.fna/target_genomes.txt --output GCF_004331455.1_ASM433145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:47,089] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:47,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75a26745-2805-445d-80e4-d7e47e8b5b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:47,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75a26745-2805-445d-80e4-d7e47e8b5b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:47,100] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:47,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:47,100] [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 zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	100.0	2141	2143	95	conclusive
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	89.5936	1580	2143	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	89.4902	1601	2143	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	89.4666	1547	2143	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	89.4621	1592	2143	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	89.1408	1548	2143	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	88.2944	1382	2143	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	86.9244	1493	2143	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.7677	996	2143	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	84.1104	1244	2143	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	83.7107	1181	2143	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.6536	1275	2143	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	83.6026	1337	2143	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.3626	493	2143	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.2144	515	2143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:47,101] [INFO] DFAST Taxonomy check result was written to GCF_004331455.1_ASM433145v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:47,102] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:47,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:47,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75a26745-2805-445d-80e4-d7e47e8b5b9a/dqc_reference/checkm_data
[2024-01-24 14:31:47,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:47,161] [INFO] Task started: CheckM
[2024-01-24 14:31:47,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331455.1_ASM433145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331455.1_ASM433145v1_genomic.fna/checkm_input GCF_004331455.1_ASM433145v1_genomic.fna/checkm_result
[2024-01-24 14:32:51,448] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:51,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:51,464] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:51,464] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:51,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331455.1_ASM433145v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:51,465] [INFO] Task started: Blastn
[2024-01-24 14:32:51,465] [INFO] Running command: blastn -query GCF_004331455.1_ASM433145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75a26745-2805-445d-80e4-d7e47e8b5b9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331455.1_ASM433145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:53,179] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:53,182] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:53,182] [INFO] Target genome list was writen to GCF_004331455.1_ASM433145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:53,189] [INFO] Task started: fastANI
[2024-01-24 14:32:53,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg57d89217-40f5-4bf6-8eed-6ecd17eb94e1/GCF_004331455.1_ASM433145v1_genomic.fna.gz --refList GCF_004331455.1_ASM433145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331455.1_ASM433145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:17,062] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:17,071] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:17,072] [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_004331455.1	s__Micromonospora zingiberis	100.0	2141	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016863515.1	s__Micromonospora gifhornensis	89.4701	1547	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.77	95.90	0.88	0.87	6	-
GCF_003583405.1	s__Micromonospora radicis	89.1341	1549	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236315.1	s__Micromonospora craterilacus	88.2637	1385	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005402585.1	s__Micromonospora sp005402585	87.9769	1533	2143	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	87.4263	1392	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236305.1	s__Micromonospora endophytica	87.1862	1321	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.96	99.96	0.99	0.98	3	-
GCF_016863555.1	s__Micromonospora qiuiae	87.0953	1382	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109115.1	s__Micromonospora phaseoli	86.9839	1528	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013364215.1	s__Micromonospora sp004307965	86.7644	1518	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_016863495.1	s__Micromonospora andamanensis	86.5311	1452	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_900112325.1	s__Micromonospora sediminimaris	86.4358	1427	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.06	96.13	0.95	0.90	3	-
GCF_010560025.1	s__Micromonospora sp010560025	86.3822	1453	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_003857055.1	s__Micromonospora inaquosa	83.2928	1194	2143	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 14:33:17,073] [INFO] GTDB search result was written to GCF_004331455.1_ASM433145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:17,073] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:17,076] [INFO] DFAST_QC result json was written to GCF_004331455.1_ASM433145v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:17,076] [INFO] DFAST_QC completed!
[2024-01-24 14:33:17,077] [INFO] Total running time: 0h2m17s