[2024-01-25 17:34:07,124] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg49586a0e-3cd4-4645-a99d-a598000d43b6/dqc_reference
[2024-01-25 17:34:09,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,027] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg56b73d35-98dc-482d-9e6b-e55bb163b4bb/GCF_020328095.1_ASM2032809v1_genomic.fna.gz | prodigal -d GCF_020328095.1_ASM2032809v1_genomic.fna/cds.fna -a GCF_020328095.1_ASM2032809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:28,045] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:28,045] [INFO] Task started: HMMsearch
[2024-01-25 17:34:28,045] [INFO] Running command: hmmsearch --tblout GCF_020328095.1_ASM2032809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49586a0e-3cd4-4645-a99d-a598000d43b6/dqc_reference/reference_markers.hmm GCF_020328095.1_ASM2032809v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:28,417] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:28,418] [INFO] Found 6/6 markers.
[2024-01-25 17:34:28,469] [INFO] Query marker FASTA was written to GCF_020328095.1_ASM2032809v1_genomic.fna/markers.fasta
[2024-01-25 17:34:28,470] [INFO] Task started: Blastn
[2024-01-25 17:34:28,470] [INFO] Running command: blastn -query GCF_020328095.1_ASM2032809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49586a0e-3cd4-4645-a99d-a598000d43b6/dqc_reference/reference_markers.fasta -out GCF_020328095.1_ASM2032809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:29,843] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:29,850] [INFO] Selected 17 target genomes.
[2024-01-25 17:34:29,850] [INFO] Target genome list was writen to GCF_020328095.1_ASM2032809v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:29,881] [INFO] Task started: fastANI
[2024-01-25 17:34:29,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b73d35-98dc-482d-9e6b-e55bb163b4bb/GCF_020328095.1_ASM2032809v1_genomic.fna.gz --refList GCF_020328095.1_ASM2032809v1_genomic.fna/target_genomes.txt --output GCF_020328095.1_ASM2032809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:02,799] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:02,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49586a0e-3cd4-4645-a99d-a598000d43b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:02,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49586a0e-3cd4-4645-a99d-a598000d43b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:02,811] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:35:02,811] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:35:02,811] [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 griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	87.5679	1613	2185	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	87.55	1613	2185	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	86.8193	1358	2185	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	86.8126	1554	2185	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	85.3908	1553	2185	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	85.337	1529	2185	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	85.2596	1525	2185	95	below_threshold
Streptomyces syringium	strain=DSM 41480	GCA_017876625.1	76729	76729	type	True	85.2247	1549	2185	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	85.133	1473	2185	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	85.1086	1470	2185	95	below_threshold
Streptomyces albireticuli	strain=NRRL B-1670	GCA_002286695.1	1940	1940	type	True	85.0725	1339	2185	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	84.9837	1518	2185	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	84.0656	1314	2185	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	83.976	1321	2185	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	83.9278	1395	2185	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	81.331	1289	2185	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.2106	1149	2185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:02,813] [INFO] DFAST Taxonomy check result was written to GCF_020328095.1_ASM2032809v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:02,814] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:02,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:02,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49586a0e-3cd4-4645-a99d-a598000d43b6/dqc_reference/checkm_data
[2024-01-25 17:35:02,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:02,878] [INFO] Task started: CheckM
[2024-01-25 17:35:02,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020328095.1_ASM2032809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020328095.1_ASM2032809v1_genomic.fna/checkm_input GCF_020328095.1_ASM2032809v1_genomic.fna/checkm_result
[2024-01-25 17:36:26,974] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:26,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:26,998] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:26,999] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:27,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020328095.1_ASM2032809v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:27,000] [INFO] Task started: Blastn
[2024-01-25 17:36:27,000] [INFO] Running command: blastn -query GCF_020328095.1_ASM2032809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49586a0e-3cd4-4645-a99d-a598000d43b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_020328095.1_ASM2032809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:29,281] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:29,285] [INFO] Selected 17 target genomes.
[2024-01-25 17:36:29,285] [INFO] Target genome list was writen to GCF_020328095.1_ASM2032809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:29,294] [INFO] Task started: fastANI
[2024-01-25 17:36:29,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b73d35-98dc-482d-9e6b-e55bb163b4bb/GCF_020328095.1_ASM2032809v1_genomic.fna.gz --refList GCF_020328095.1_ASM2032809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020328095.1_ASM2032809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:01,191] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:01,202] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:01,202] [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_014650495.1	s__Streptomyces cinnamoneus	95.4079	1920	2185	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	87.5589	1612	2185	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	87.4097	1619	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCA_000715685.1	s__Streptomyces lilacinus	87.202	1573	2185	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	86.9677	1525	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	86.8284	1357	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648775.1	s__Streptomyces abikoensis	86.8191	1553	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	-
GCF_014203545.1	s__Streptomyces netropsis	85.4283	1546	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003011965.1	s__Streptomyces nondiastaticus	85.2602	1469	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_017876625.1	s__Streptomyces syringium	85.1993	1553	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	-
GCF_002891295.1	s__Streptomyces eurocidicus	85.1463	1473	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	3	-
GCF_003391135.1	s__Streptomyces olivoreticuli	85.101	1445	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286695.1	s__Streptomyces albireticuli	85.015	1347	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013055795.1	s__Streptomyces sp013055795	84.3263	1346	2185	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	84.2939	1350	2185	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	83.9074	1399	2185	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	83.8323	1407	2185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:01,203] [INFO] GTDB search result was written to GCF_020328095.1_ASM2032809v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:01,204] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:01,208] [INFO] DFAST_QC result json was written to GCF_020328095.1_ASM2032809v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:01,208] [INFO] DFAST_QC completed!
[2024-01-25 17:37:01,208] [INFO] Total running time: 0h2m54s