[2024-01-24 11:26:12,925] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ea13a32-3078-42b9-8688-9f24dcda571a/dqc_reference
[2024-01-24 11:26:14,371] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,372] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,372] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ad43f81-433f-466b-974c-f4cc9ed9da07/GCF_014203555.1_ASM1420355v1_genomic.fna.gz | prodigal -d GCF_014203555.1_ASM1420355v1_genomic.fna/cds.fna -a GCF_014203555.1_ASM1420355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:30,533] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:30,533] [INFO] Task started: HMMsearch
[2024-01-24 11:26:30,534] [INFO] Running command: hmmsearch --tblout GCF_014203555.1_ASM1420355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ea13a32-3078-42b9-8688-9f24dcda571a/dqc_reference/reference_markers.hmm GCF_014203555.1_ASM1420355v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:30,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:30,902] [INFO] Found 6/6 markers.
[2024-01-24 11:26:30,953] [INFO] Query marker FASTA was written to GCF_014203555.1_ASM1420355v1_genomic.fna/markers.fasta
[2024-01-24 11:26:30,953] [INFO] Task started: Blastn
[2024-01-24 11:26:30,953] [INFO] Running command: blastn -query GCF_014203555.1_ASM1420355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea13a32-3078-42b9-8688-9f24dcda571a/dqc_reference/reference_markers.fasta -out GCF_014203555.1_ASM1420355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:32,415] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:32,418] [INFO] Selected 22 target genomes.
[2024-01-24 11:26:32,419] [INFO] Target genome list was writen to GCF_014203555.1_ASM1420355v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:32,427] [INFO] Task started: fastANI
[2024-01-24 11:26:32,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ad43f81-433f-466b-974c-f4cc9ed9da07/GCF_014203555.1_ASM1420355v1_genomic.fna.gz --refList GCF_014203555.1_ASM1420355v1_genomic.fna/target_genomes.txt --output GCF_014203555.1_ASM1420355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:14,596] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:14,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ea13a32-3078-42b9-8688-9f24dcda571a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:14,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ea13a32-3078-42b9-8688-9f24dcda571a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:14,617] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:14,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:14,618] [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 olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	100.0	1841	1841	95	conclusive
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	87.2146	1395	1841	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	87.1723	1407	1841	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	86.4855	1387	1841	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	85.9637	1363	1841	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	85.9448	1297	1841	95	below_threshold
Streptomyces syringium	strain=DSM 41480	GCA_017876625.1	76729	76729	type	True	85.888	1398	1841	95	below_threshold
Streptomyces netropsis	strain=JCM 4063	GCA_014648835.1	55404	55404	type	True	85.8805	1377	1841	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	85.849	1389	1841	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	85.4992	1401	1841	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	85.495	1412	1841	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	85.4413	1401	1841	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	85.433	1386	1841	95	below_threshold
Streptomyces eurocidicus	strain=CECT 3259	GCA_014203505.1	66423	66423	type	True	85.4329	1399	1841	95	below_threshold
Streptomyces albireticuli	strain=NRRL B-1670	GCA_002286695.1	1940	1940	type	True	85.4173	1226	1841	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	85.4132	1380	1841	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	85.3694	1406	1841	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	84.482	1211	1841	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	84.4013	1310	1841	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	84.3558	1197	1841	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	81.8799	1202	1841	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.2808	1103	1841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:14,620] [INFO] DFAST Taxonomy check result was written to GCF_014203555.1_ASM1420355v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:14,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:14,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:14,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ea13a32-3078-42b9-8688-9f24dcda571a/dqc_reference/checkm_data
[2024-01-24 11:27:14,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:14,676] [INFO] Task started: CheckM
[2024-01-24 11:27:14,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203555.1_ASM1420355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203555.1_ASM1420355v1_genomic.fna/checkm_input GCF_014203555.1_ASM1420355v1_genomic.fna/checkm_result
[2024-01-24 11:28:08,735] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:08,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:08,761] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:08,762] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:08,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203555.1_ASM1420355v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:08,762] [INFO] Task started: Blastn
[2024-01-24 11:28:08,763] [INFO] Running command: blastn -query GCF_014203555.1_ASM1420355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea13a32-3078-42b9-8688-9f24dcda571a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203555.1_ASM1420355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:10,978] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:10,983] [INFO] Selected 20 target genomes.
[2024-01-24 11:28:10,983] [INFO] Target genome list was writen to GCF_014203555.1_ASM1420355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:10,999] [INFO] Task started: fastANI
[2024-01-24 11:28:10,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ad43f81-433f-466b-974c-f4cc9ed9da07/GCF_014203555.1_ASM1420355v1_genomic.fna.gz --refList GCF_014203555.1_ASM1420355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203555.1_ASM1420355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:44,495] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:44,516] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:44,516] [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_014203555.1	s__Streptomyces olivoverticillatus	100.0	1841	1841	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	87.2277	1394	1841	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	86.9306	1433	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCF_014650495.1	s__Streptomyces cinnamoneus	86.9118	1406	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939475.1	s__Streptomyces cinnamoneus_A	86.8127	1396	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014648775.1	s__Streptomyces abikoensis	86.456	1392	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	-
GCF_013030945.1	s__Streptomyces morookaense	85.9272	1299	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018614525.1	s__Streptomyces sp018614525	85.718	1264	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719265.1	s__Streptomyces roseoverticillatus	85.629	1360	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_003391135.1	s__Streptomyces olivoreticuli	85.5769	1419	1841	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	85.5059	1411	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.88	0.88	2	-
GCF_002891295.1	s__Streptomyces eurocidicus	85.4525	1399	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	3	-
GCF_003626645.1	s__Streptomyces klenkii	85.4486	1383	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	99.37	0.96	0.96	2	-
GCF_013055795.1	s__Streptomyces sp013055795	84.6731	1283	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	84.4014	1310	1841	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	84.3716	1295	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	82.4522	1178	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000717595.1	s__Streptomyces flavochromogenes	81.5679	1086	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	81.2463	1072	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCF_014646115.1	s__Streptomyces camponoticapitis	81.0643	979	1841	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 11:28:44,518] [INFO] GTDB search result was written to GCF_014203555.1_ASM1420355v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:44,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:44,523] [INFO] DFAST_QC result json was written to GCF_014203555.1_ASM1420355v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:44,523] [INFO] DFAST_QC completed!
[2024-01-24 11:28:44,523] [INFO] Total running time: 0h2m32s