[2024-01-24 12:15:18,796] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,799] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,799] [INFO] DQC Reference Directory: /var/lib/cwl/stgcaa31249-d3d4-4c28-ac0f-033733f6baea/dqc_reference
[2024-01-24 12:15:20,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,076] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,076] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb11a008-ef41-4f10-a574-eaee7c4aaa93/GCF_016428645.1_ASM1642864v1_genomic.fna.gz | prodigal -d GCF_016428645.1_ASM1642864v1_genomic.fna/cds.fna -a GCF_016428645.1_ASM1642864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:33,833] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:33,834] [INFO] Task started: HMMsearch
[2024-01-24 12:15:33,834] [INFO] Running command: hmmsearch --tblout GCF_016428645.1_ASM1642864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcaa31249-d3d4-4c28-ac0f-033733f6baea/dqc_reference/reference_markers.hmm GCF_016428645.1_ASM1642864v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:34,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:34,136] [INFO] Found 6/6 markers.
[2024-01-24 12:15:34,190] [INFO] Query marker FASTA was written to GCF_016428645.1_ASM1642864v1_genomic.fna/markers.fasta
[2024-01-24 12:15:34,190] [INFO] Task started: Blastn
[2024-01-24 12:15:34,190] [INFO] Running command: blastn -query GCF_016428645.1_ASM1642864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaa31249-d3d4-4c28-ac0f-033733f6baea/dqc_reference/reference_markers.fasta -out GCF_016428645.1_ASM1642864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:35,320] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:35,326] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:35,327] [INFO] Target genome list was writen to GCF_016428645.1_ASM1642864v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:35,333] [INFO] Task started: fastANI
[2024-01-24 12:15:35,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb11a008-ef41-4f10-a574-eaee7c4aaa93/GCF_016428645.1_ASM1642864v1_genomic.fna.gz --refList GCF_016428645.1_ASM1642864v1_genomic.fna/target_genomes.txt --output GCF_016428645.1_ASM1642864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:52,191] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:52,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcaa31249-d3d4-4c28-ac0f-033733f6baea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:52,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcaa31249-d3d4-4c28-ac0f-033733f6baea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:52,204] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:52,204] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:52,205] [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
Glycomyces salinus	strain=YIM 93776	GCA_016428645.1	980294	980294	type	True	100.0	1687	1693	95	conclusive
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	84.0681	986	1693	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	83.7664	1063	1693	95	below_threshold
Glycomyces tenuis	strain=DSM 44171	GCA_000427885.1	58116	58116	type	True	83.7633	1113	1693	95	below_threshold
Glycomyces tenuis	strain=NRRL B-16895	GCA_000715885.1	58116	58116	type	True	83.7134	1130	1693	95	below_threshold
Glycomyces buryatensis	strain=18	GCA_004912275.1	2570927	2570927	type	True	82.5911	1023	1693	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	82.3563	1016	1693	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	82.3397	935	1693	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	82.2665	998	1693	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	82.1283	1012	1693	95	below_threshold
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	76.8214	408	1693	95	below_threshold
Micromonospora yangpuensis	strain=CGMCC 4.5736	GCA_014645775.1	683228	683228	type	True	76.8077	398	1693	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	76.4245	217	1693	95	below_threshold
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	76.1521	480	1693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:52,208] [INFO] DFAST Taxonomy check result was written to GCF_016428645.1_ASM1642864v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:52,208] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:52,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:52,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcaa31249-d3d4-4c28-ac0f-033733f6baea/dqc_reference/checkm_data
[2024-01-24 12:15:52,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:52,262] [INFO] Task started: CheckM
[2024-01-24 12:15:52,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016428645.1_ASM1642864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016428645.1_ASM1642864v1_genomic.fna/checkm_input GCF_016428645.1_ASM1642864v1_genomic.fna/checkm_result
[2024-01-24 12:16:33,016] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:33,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:33,040] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:33,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:33,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016428645.1_ASM1642864v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:33,041] [INFO] Task started: Blastn
[2024-01-24 12:16:33,042] [INFO] Running command: blastn -query GCF_016428645.1_ASM1642864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaa31249-d3d4-4c28-ac0f-033733f6baea/dqc_reference/reference_markers_gtdb.fasta -out GCF_016428645.1_ASM1642864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:34,606] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:34,610] [INFO] Selected 12 target genomes.
[2024-01-24 12:16:34,611] [INFO] Target genome list was writen to GCF_016428645.1_ASM1642864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:34,620] [INFO] Task started: fastANI
[2024-01-24 12:16:34,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb11a008-ef41-4f10-a574-eaee7c4aaa93/GCF_016428645.1_ASM1642864v1_genomic.fna.gz --refList GCF_016428645.1_ASM1642864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016428645.1_ASM1642864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:48,984] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:49,006] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:49,006] [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_016428645.1	s__Glycomyces sp016428645	100.0	1687	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002798405.1	s__Glycomyces xiaoerkulensis	84.0667	987	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427885.1	s__Glycomyces tenuis	83.7677	1114	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482705.1	s__Glycomyces arizonensis	83.755	1064	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912275.1	s__Glycomyces buryatensis	82.575	1027	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933745.1	s__Glycomyces terrestris	82.3997	1010	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265355.1	s__Glycomyces dulcitolivorans	82.3645	932	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101745.1	s__Glycomyces harbinensis	82.3537	1077	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009451885.1	s__Glycomyces albidus	82.3005	994	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102815.1	s__Glycomyces sambucus	82.1284	1012	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091615.1	s__Micromonospora yangpuensis	76.8134	407	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731615.1	s__Mycobacterium insubricum	76.4081	219	1693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:49,009] [INFO] GTDB search result was written to GCF_016428645.1_ASM1642864v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:49,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:49,013] [INFO] DFAST_QC result json was written to GCF_016428645.1_ASM1642864v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:49,013] [INFO] DFAST_QC completed!
[2024-01-24 12:16:49,013] [INFO] Total running time: 0h1m30s