[2024-01-24 13:55:47,367] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:47,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:47,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3d205d0-507d-46ed-a1dc-7e21e9a163d6/dqc_reference
[2024-01-24 13:55:48,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:48,740] [INFO] Task started: Prodigal
[2024-01-24 13:55:48,740] [INFO] Running command: gunzip -c /var/lib/cwl/stgf77eef6a-d0d3-4516-b199-7dc4ff891288/GCF_014654785.1_ASM1465478v1_genomic.fna.gz | prodigal -d GCF_014654785.1_ASM1465478v1_genomic.fna/cds.fna -a GCF_014654785.1_ASM1465478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:10,786] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:10,787] [INFO] Task started: HMMsearch
[2024-01-24 13:56:10,787] [INFO] Running command: hmmsearch --tblout GCF_014654785.1_ASM1465478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3d205d0-507d-46ed-a1dc-7e21e9a163d6/dqc_reference/reference_markers.hmm GCF_014654785.1_ASM1465478v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:11,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:11,128] [INFO] Found 6/6 markers.
[2024-01-24 13:56:11,190] [INFO] Query marker FASTA was written to GCF_014654785.1_ASM1465478v1_genomic.fna/markers.fasta
[2024-01-24 13:56:11,191] [INFO] Task started: Blastn
[2024-01-24 13:56:11,191] [INFO] Running command: blastn -query GCF_014654785.1_ASM1465478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3d205d0-507d-46ed-a1dc-7e21e9a163d6/dqc_reference/reference_markers.fasta -out GCF_014654785.1_ASM1465478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:12,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:12,591] [INFO] Selected 20 target genomes.
[2024-01-24 13:56:12,592] [INFO] Target genome list was writen to GCF_014654785.1_ASM1465478v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:12,616] [INFO] Task started: fastANI
[2024-01-24 13:56:12,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgf77eef6a-d0d3-4516-b199-7dc4ff891288/GCF_014654785.1_ASM1465478v1_genomic.fna.gz --refList GCF_014654785.1_ASM1465478v1_genomic.fna/target_genomes.txt --output GCF_014654785.1_ASM1465478v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:49,195] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:49,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3d205d0-507d-46ed-a1dc-7e21e9a163d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:49,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3d205d0-507d-46ed-a1dc-7e21e9a163d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:49,211] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:49,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:49,211] [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 mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	100.0	2392	2396	95	conclusive
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	85.4675	1592	2396	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	85.4577	1608	2396	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	85.2529	1343	2396	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	85.1521	1537	2396	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	84.2236	1401	2396	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	84.1844	1429	2396	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	84.0844	1501	2396	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	83.9334	1508	2396	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	83.8843	1547	2396	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	83.8654	1423	2396	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	83.7691	1498	2396	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	83.7404	1378	2396	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	83.6455	1432	2396	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.2845	1089	2396	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	80.993	1119	2396	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	80.8795	1069	2396	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.8615	1319	2396	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	74.8749	115	2396	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	74.8586	130	2396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:49,213] [INFO] DFAST Taxonomy check result was written to GCF_014654785.1_ASM1465478v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:49,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:49,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:49,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3d205d0-507d-46ed-a1dc-7e21e9a163d6/dqc_reference/checkm_data
[2024-01-24 13:56:49,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:49,280] [INFO] Task started: CheckM
[2024-01-24 13:56:49,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014654785.1_ASM1465478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014654785.1_ASM1465478v1_genomic.fna/checkm_input GCF_014654785.1_ASM1465478v1_genomic.fna/checkm_result
[2024-01-24 13:58:15,555] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:15,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:15,588] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:15,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:15,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014654785.1_ASM1465478v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:15,589] [INFO] Task started: Blastn
[2024-01-24 13:58:15,589] [INFO] Running command: blastn -query GCF_014654785.1_ASM1465478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3d205d0-507d-46ed-a1dc-7e21e9a163d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014654785.1_ASM1465478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:18,110] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:18,113] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:18,114] [INFO] Target genome list was writen to GCF_014654785.1_ASM1465478v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:18,141] [INFO] Task started: fastANI
[2024-01-24 13:58:18,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgf77eef6a-d0d3-4516-b199-7dc4ff891288/GCF_014654785.1_ASM1465478v1_genomic.fna.gz --refList GCF_014654785.1_ASM1465478v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014654785.1_ASM1465478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:05,032] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:05,049] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:05,050] [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_014654785.1	s__Streptomyces mashuensis	100.0	2392	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014655595.1	s__Streptomyces griseocarneus	85.4832	1603	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	85.4016	1510	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715685.1	s__Streptomyces lilacinus	85.3241	1526	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	85.3051	1337	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349075.1	s__Streptomyces triculaminicus_A	85.2126	1570	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCF_014648775.1	s__Streptomyces abikoensis	85.1275	1541	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	-
GCF_002939475.1	s__Streptomyces cinnamoneus_A	84.9755	1546	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013030945.1	s__Streptomyces morookaense	84.1862	1407	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003011965.1	s__Streptomyces nondiastaticus	84.1607	1445	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_003626645.1	s__Streptomyces klenkii	84.1264	1494	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	99.37	0.96	0.96	2	-
GCF_014650335.1	s__Streptomyces hiroshimensis	83.8915	1513	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187435.1	s__Streptomyces caatingaensis	83.8904	1419	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001445655.1	s__Streptomyces roseifaciens	83.8814	1549	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.88	0.88	2	-
GCF_017916255.1	s__Streptomyces mobaraensis	83.6934	1424	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_014253015.1	s__Streptomyces sp014253015	83.625	1414	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999245.1	s__Streptomyces sp015999245	83.5885	1390	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007176755.1	s__Streptomyces sp007176755	81.0743	1191	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	80.9439	1128	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_001418325.1	s__Streptomyces atriruber	80.9292	1060	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	80.831	1242	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495685.1	s__Streptomyces sp014495685	80.4847	1114	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	80.4062	1152	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,052] [INFO] GTDB search result was written to GCF_014654785.1_ASM1465478v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:05,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:05,057] [INFO] DFAST_QC result json was written to GCF_014654785.1_ASM1465478v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:05,057] [INFO] DFAST_QC completed!
[2024-01-24 13:59:05,057] [INFO] Total running time: 0h3m18s