[2024-01-24 11:59:22,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgcca6ba8b-aa88-4261-b2d1-cab3c178f5e4/dqc_reference
[2024-01-24 11:59:25,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,646] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg207887f4-e56e-405e-9526-2c465430ebf4/GCF_014649335.1_ASM1464933v1_genomic.fna.gz | prodigal -d GCF_014649335.1_ASM1464933v1_genomic.fna/cds.fna -a GCF_014649335.1_ASM1464933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:43,358] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:43,359] [INFO] Task started: HMMsearch
[2024-01-24 11:59:43,359] [INFO] Running command: hmmsearch --tblout GCF_014649335.1_ASM1464933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcca6ba8b-aa88-4261-b2d1-cab3c178f5e4/dqc_reference/reference_markers.hmm GCF_014649335.1_ASM1464933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:43,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:43,682] [INFO] Found 6/6 markers.
[2024-01-24 11:59:43,737] [INFO] Query marker FASTA was written to GCF_014649335.1_ASM1464933v1_genomic.fna/markers.fasta
[2024-01-24 11:59:43,737] [INFO] Task started: Blastn
[2024-01-24 11:59:43,737] [INFO] Running command: blastn -query GCF_014649335.1_ASM1464933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcca6ba8b-aa88-4261-b2d1-cab3c178f5e4/dqc_reference/reference_markers.fasta -out GCF_014649335.1_ASM1464933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:45,090] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:45,093] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:45,094] [INFO] Target genome list was writen to GCF_014649335.1_ASM1464933v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:45,107] [INFO] Task started: fastANI
[2024-01-24 11:59:45,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg207887f4-e56e-405e-9526-2c465430ebf4/GCF_014649335.1_ASM1464933v1_genomic.fna.gz --refList GCF_014649335.1_ASM1464933v1_genomic.fna/target_genomes.txt --output GCF_014649335.1_ASM1464933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:13,288] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:13,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcca6ba8b-aa88-4261-b2d1-cab3c178f5e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:13,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcca6ba8b-aa88-4261-b2d1-cab3c178f5e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:13,307] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:13,308] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:13,308] [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
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	100.0	2243	2244	95	conclusive
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	91.0013	1345	2244	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	90.6504	1395	2244	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	89.1799	1649	2244	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	89.1456	1689	2244	95	below_threshold
Streptomyces fradiae	strain=DSM 40063	GCA_002119225.1	1906	1906	suspected-type	True	89.0904	1540	2244	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	88.9912	1024	2244	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	84.6356	1490	2244	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	83.3801	1382	2244	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	83.1568	1367	2244	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.1051	1310	2244	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	82.7498	1294	2244	95	below_threshold
Streptomyces marianii	strain=ICN19	GCA_005795905.1	1817406	1817406	type	True	82.5388	1305	2244	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.715	1325	2244	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	74.8164	113	2244	95	below_threshold
Limnochorda pilosa	strain=HC45	GCA_001544015.1	1555112	1555112	type	True	74.8145	131	2244	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	74.7463	126	2244	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	74.739	146	2244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:13,309] [INFO] DFAST Taxonomy check result was written to GCF_014649335.1_ASM1464933v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:13,310] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:13,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:13,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcca6ba8b-aa88-4261-b2d1-cab3c178f5e4/dqc_reference/checkm_data
[2024-01-24 12:00:13,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:13,381] [INFO] Task started: CheckM
[2024-01-24 12:00:13,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649335.1_ASM1464933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649335.1_ASM1464933v1_genomic.fna/checkm_input GCF_014649335.1_ASM1464933v1_genomic.fna/checkm_result
[2024-01-24 12:01:40,370] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:40,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:40,396] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:40,397] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:40,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649335.1_ASM1464933v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:40,398] [INFO] Task started: Blastn
[2024-01-24 12:01:40,398] [INFO] Running command: blastn -query GCF_014649335.1_ASM1464933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcca6ba8b-aa88-4261-b2d1-cab3c178f5e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649335.1_ASM1464933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:42,597] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:42,601] [INFO] Selected 12 target genomes.
[2024-01-24 12:01:42,601] [INFO] Target genome list was writen to GCF_014649335.1_ASM1464933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:42,609] [INFO] Task started: fastANI
[2024-01-24 12:01:42,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg207887f4-e56e-405e-9526-2c465430ebf4/GCF_014649335.1_ASM1464933v1_genomic.fna.gz --refList GCF_014649335.1_ASM1464933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649335.1_ASM1464933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:03,661] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:03,680] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:03,681] [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_014649335.1	s__Streptomyces roseolilacinus	100.0	2243	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012396115.1	s__Streptomyces somaliensis	91.0009	1063	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000258595.1	s__Streptomyces somaliensis_A	90.6939	1293	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478605.2	s__Streptomyces thermolilacinus	90.2685	1730	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704425.1	s__Streptomyces fradiae	89.1867	1684	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_008271805.1	s__Streptomyces sp008271805	87.6227	1456	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013362995.1	s__Streptomyces sp013362995	87.0238	1357	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649735.1	s__Streptomyces lavendofoliae	84.6346	1490	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650175.1	s__Streptomyces termitum	83.4843	1357	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000720535.1	s__Streptomyces halstedii	81.8766	1278	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	96.54	0.92	0.83	17	-
GCF_000719865.1	s__Streptomyces albus_E	81.0646	1176	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	78.8503	946	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:03,682] [INFO] GTDB search result was written to GCF_014649335.1_ASM1464933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:03,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:03,686] [INFO] DFAST_QC result json was written to GCF_014649335.1_ASM1464933v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:03,687] [INFO] DFAST_QC completed!
[2024-01-24 12:02:03,687] [INFO] Total running time: 0h2m41s