[2024-01-24 11:26:54,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,314] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg5066bd50-f6ce-42d2-9a63-3cf5cf39e199/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,223] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg62ebca22-427d-419d-ae3a-cff483337d19/GCF_015751765.1_ASM1575176v1_genomic.fna.gz | prodigal -d GCF_015751765.1_ASM1575176v1_genomic.fna/cds.fna -a GCF_015751765.1_ASM1575176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:19,411] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:19,412] [INFO] Task started: HMMsearch
[2024-01-24 11:27:19,412] [INFO] Running command: hmmsearch --tblout GCF_015751765.1_ASM1575176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5066bd50-f6ce-42d2-9a63-3cf5cf39e199/dqc_reference/reference_markers.hmm GCF_015751765.1_ASM1575176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:19,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:19,761] [INFO] Found 6/6 markers.
[2024-01-24 11:27:19,819] [INFO] Query marker FASTA was written to GCF_015751765.1_ASM1575176v1_genomic.fna/markers.fasta
[2024-01-24 11:27:19,820] [INFO] Task started: Blastn
[2024-01-24 11:27:19,820] [INFO] Running command: blastn -query GCF_015751765.1_ASM1575176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5066bd50-f6ce-42d2-9a63-3cf5cf39e199/dqc_reference/reference_markers.fasta -out GCF_015751765.1_ASM1575176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:21,009] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:21,013] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:21,014] [INFO] Target genome list was writen to GCF_015751765.1_ASM1575176v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:21,020] [INFO] Task started: fastANI
[2024-01-24 11:27:21,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg62ebca22-427d-419d-ae3a-cff483337d19/GCF_015751765.1_ASM1575176v1_genomic.fna.gz --refList GCF_015751765.1_ASM1575176v1_genomic.fna/target_genomes.txt --output GCF_015751765.1_ASM1575176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:49,589] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:49,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5066bd50-f6ce-42d2-9a63-3cf5cf39e199/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:49,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5066bd50-f6ce-42d2-9a63-3cf5cf39e199/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:49,606] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:49,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:49,607] [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 ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	100.0	2364	2365	95	conclusive
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	93.9469	1972	2365	95	below_threshold
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	93.8887	1895	2365	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	93.8084	2027	2365	95	below_threshold
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	93.6742	1773	2365	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	92.9235	1720	2365	95	below_threshold
Micromonospora violae	strain=DSM 45888	GCA_004217135.1	1278207	1278207	type	True	92.4763	1874	2365	95	below_threshold
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	90.8314	1796	2365	95	below_threshold
Micromonospora parathelypteridis	strain=CGMCC 4.7347	GCA_014646315.1	1839617	1839617	type	True	90.4599	1799	2365	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	90.4332	1817	2365	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	89.2841	1593	2365	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	88.8273	1511	2365	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.1472	1116	2365	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.0108	1413	2365	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.8464	1405	2365	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.2529	1331	2365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:49,608] [INFO] DFAST Taxonomy check result was written to GCF_015751765.1_ASM1575176v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:49,609] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:49,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:49,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5066bd50-f6ce-42d2-9a63-3cf5cf39e199/dqc_reference/checkm_data
[2024-01-24 11:27:49,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:49,679] [INFO] Task started: CheckM
[2024-01-24 11:27:49,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015751765.1_ASM1575176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015751765.1_ASM1575176v1_genomic.fna/checkm_input GCF_015751765.1_ASM1575176v1_genomic.fna/checkm_result
[2024-01-24 11:29:08,352] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:08,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:08,378] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:08,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:08,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015751765.1_ASM1575176v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:08,380] [INFO] Task started: Blastn
[2024-01-24 11:29:08,380] [INFO] Running command: blastn -query GCF_015751765.1_ASM1575176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5066bd50-f6ce-42d2-9a63-3cf5cf39e199/dqc_reference/reference_markers_gtdb.fasta -out GCF_015751765.1_ASM1575176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:10,135] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:10,140] [INFO] Selected 12 target genomes.
[2024-01-24 11:29:10,140] [INFO] Target genome list was writen to GCF_015751765.1_ASM1575176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:10,149] [INFO] Task started: fastANI
[2024-01-24 11:29:10,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg62ebca22-427d-419d-ae3a-cff483337d19/GCF_015751765.1_ASM1575176v1_genomic.fna.gz --refList GCF_015751765.1_ASM1575176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015751765.1_ASM1575176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:32,349] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:32,360] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:32,360] [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_015751765.1	s__Micromonospora ureilytica	100.0	2363	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	97.34	0.88	0.87	3	conclusive
GCF_900091575.1	s__Micromonospora saelicesensis	93.9667	1970	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_018070325.1	s__Micromonospora sp018070325	93.9091	1893	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_003264365.1	s__Micromonospora noduli	93.8685	1897	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.92	97.90	0.94	0.91	8	-
GCF_015751785.1	s__Micromonospora vinacea	93.807	2027	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003857035.1	s__Micromonospora arida	93.6742	1773	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.1103	N/A	N/A	N/A	N/A	1	-
GCF_003857055.1	s__Micromonospora inaquosa	92.9271	1721	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718515.1	s__Micromonospora parva	92.7427	1869	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.24	99.24	0.97	0.97	2	-
GCF_004217135.1	s__Micromonospora violae	92.4932	1872	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201145.1	s__Micromonospora parathelypteridis	90.4174	1819	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003205615.1	s__Micromonospora arborensis	90.3166	1763	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228125.1	s__Micromonospora orduensis	89.2736	1594	2365	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 11:29:32,362] [INFO] GTDB search result was written to GCF_015751765.1_ASM1575176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:32,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:32,366] [INFO] DFAST_QC result json was written to GCF_015751765.1_ASM1575176v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:32,366] [INFO] DFAST_QC completed!
[2024-01-24 11:29:32,366] [INFO] Total running time: 0h2m38s