[2024-01-24 13:56:27,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg7eeb22ec-7088-40e0-928d-838e1ec10035/dqc_reference
[2024-01-24 13:56:28,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,809] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg796f9f5f-c038-43ba-99fc-be6278c140a5/GCF_014649195.1_ASM1464919v1_genomic.fna.gz | prodigal -d GCF_014649195.1_ASM1464919v1_genomic.fna/cds.fna -a GCF_014649195.1_ASM1464919v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:56,006] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:56,007] [INFO] Task started: HMMsearch
[2024-01-24 13:56:56,007] [INFO] Running command: hmmsearch --tblout GCF_014649195.1_ASM1464919v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7eeb22ec-7088-40e0-928d-838e1ec10035/dqc_reference/reference_markers.hmm GCF_014649195.1_ASM1464919v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:56,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:56,383] [INFO] Found 6/6 markers.
[2024-01-24 13:56:56,460] [INFO] Query marker FASTA was written to GCF_014649195.1_ASM1464919v1_genomic.fna/markers.fasta
[2024-01-24 13:56:56,461] [INFO] Task started: Blastn
[2024-01-24 13:56:56,461] [INFO] Running command: blastn -query GCF_014649195.1_ASM1464919v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eeb22ec-7088-40e0-928d-838e1ec10035/dqc_reference/reference_markers.fasta -out GCF_014649195.1_ASM1464919v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:57,790] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:57,795] [INFO] Selected 13 target genomes.
[2024-01-24 13:56:57,795] [INFO] Target genome list was writen to GCF_014649195.1_ASM1464919v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:57,809] [INFO] Task started: fastANI
[2024-01-24 13:56:57,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg796f9f5f-c038-43ba-99fc-be6278c140a5/GCF_014649195.1_ASM1464919v1_genomic.fna.gz --refList GCF_014649195.1_ASM1464919v1_genomic.fna/target_genomes.txt --output GCF_014649195.1_ASM1464919v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:28,536] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:28,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7eeb22ec-7088-40e0-928d-838e1ec10035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:28,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7eeb22ec-7088-40e0-928d-838e1ec10035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:28,548] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:28,548] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:28,548] [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 coeruleorubidus	strain=JCM 4359	GCA_014649455.1	116188	116188	suspected-type	True	97.9848	2793	3103	95	conclusive
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	97.9777	2831	3103	95	conclusive
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	94.9809	2094	3103	95	below_threshold
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	94.9486	2286	3103	95	below_threshold
Streptomyces caelestis	strain=DSM 40084	GCA_014205255.1	36816	36816	type	True	93.8037	2354	3103	95	below_threshold
Streptomyces caelestis	strain=JCM 4566	GCA_014650295.1	36816	36816	type	True	93.7884	2346	3103	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	93.3611	2118	3103	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.7367	2298	3103	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	91.4401	2387	3103	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.3024	1829	3103	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	90.2329	2067	3103	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	89.9477	1933	3103	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.4932	1760	3103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:28,550] [INFO] DFAST Taxonomy check result was written to GCF_014649195.1_ASM1464919v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:28,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:28,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:28,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7eeb22ec-7088-40e0-928d-838e1ec10035/dqc_reference/checkm_data
[2024-01-24 13:57:28,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:28,652] [INFO] Task started: CheckM
[2024-01-24 13:57:28,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649195.1_ASM1464919v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649195.1_ASM1464919v1_genomic.fna/checkm_input GCF_014649195.1_ASM1464919v1_genomic.fna/checkm_result
[2024-01-24 13:59:43,648] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:43,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:43,681] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:43,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:43,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649195.1_ASM1464919v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:43,683] [INFO] Task started: Blastn
[2024-01-24 13:59:43,683] [INFO] Running command: blastn -query GCF_014649195.1_ASM1464919v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eeb22ec-7088-40e0-928d-838e1ec10035/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649195.1_ASM1464919v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:45,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:45,937] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:45,937] [INFO] Target genome list was writen to GCF_014649195.1_ASM1464919v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:45,956] [INFO] Task started: fastANI
[2024-01-24 13:59:45,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg796f9f5f-c038-43ba-99fc-be6278c140a5/GCF_014649195.1_ASM1464919v1_genomic.fna.gz --refList GCF_014649195.1_ASM1464919v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649195.1_ASM1464919v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:08,500] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:08,509] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:08,509] [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_008705135.1	s__Streptomyces coeruleorubidus	97.9695	2832	3103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	conclusive
GCF_002148965.1	s__Streptomyces swartbergensis	94.9884	2094	3103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000415505.1	s__Streptomyces afghaniensis	93.9509	2291	3103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205255.1	s__Streptomyces caelestis	93.826	2351	3103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900236475.1	s__Streptomyces chartreusis_D	93.6036	2390	3103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_002150735.1	s__Streptomyces africanus	93.3555	2120	3103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158955.1	s__Streptomyces viridochromogenes_B	90.968	2231	3103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	85.9188	1782	3103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364215.1	s__Streptomyces sp004364215	85.8156	2092	3103	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 14:00:08,511] [INFO] GTDB search result was written to GCF_014649195.1_ASM1464919v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:08,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:08,515] [INFO] DFAST_QC result json was written to GCF_014649195.1_ASM1464919v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:08,516] [INFO] DFAST_QC completed!
[2024-01-24 14:00:08,516] [INFO] Total running time: 0h3m41s