[2024-01-24 14:53:50,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg369c2ea5-6156-4d95-8a31-7b9ec5131956/dqc_reference
[2024-01-24 14:53:51,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,577] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e804b0b-9515-4e76-8913-cdfa1b2f141a/GCF_006636205.1_ASM663620v1_genomic.fna.gz | prodigal -d GCF_006636205.1_ASM663620v1_genomic.fna/cds.fna -a GCF_006636205.1_ASM663620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:18,344] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:18,344] [INFO] Task started: HMMsearch
[2024-01-24 14:54:18,344] [INFO] Running command: hmmsearch --tblout GCF_006636205.1_ASM663620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg369c2ea5-6156-4d95-8a31-7b9ec5131956/dqc_reference/reference_markers.hmm GCF_006636205.1_ASM663620v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:18,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:18,725] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e804b0b-9515-4e76-8913-cdfa1b2f141a/GCF_006636205.1_ASM663620v1_genomic.fna.gz]
[2024-01-24 14:54:18,794] [INFO] Query marker FASTA was written to GCF_006636205.1_ASM663620v1_genomic.fna/markers.fasta
[2024-01-24 14:54:18,795] [INFO] Task started: Blastn
[2024-01-24 14:54:18,795] [INFO] Running command: blastn -query GCF_006636205.1_ASM663620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg369c2ea5-6156-4d95-8a31-7b9ec5131956/dqc_reference/reference_markers.fasta -out GCF_006636205.1_ASM663620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:20,141] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:20,147] [INFO] Selected 14 target genomes.
[2024-01-24 14:54:20,148] [INFO] Target genome list was writen to GCF_006636205.1_ASM663620v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:20,155] [INFO] Task started: fastANI
[2024-01-24 14:54:20,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e804b0b-9515-4e76-8913-cdfa1b2f141a/GCF_006636205.1_ASM663620v1_genomic.fna.gz --refList GCF_006636205.1_ASM663620v1_genomic.fna/target_genomes.txt --output GCF_006636205.1_ASM663620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:49,438] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:49,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg369c2ea5-6156-4d95-8a31-7b9ec5131956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:49,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg369c2ea5-6156-4d95-8a31-7b9ec5131956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:49,461] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:49,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:49,462] [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
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	100.0	2856	2858	95	conclusive
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	91.6902	1914	2858	95	below_threshold
Kitasatospora viridis	strain=DSM 44826	GCA_007829815.1	281105	281105	type	True	86.3072	1845	2858	95	below_threshold
Kitasatospora azatica	strain=KCTC 9699	GCA_000744785.1	58347	58347	type	True	85.9639	1613	2858	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	84.881	1705	2858	95	below_threshold
Kitasatospora gansuensis	strain=DSM 44786	GCA_014203705.1	258050	258050	type	True	82.794	1370	2858	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	82.6145	1470	2858	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	82.373	1430	2858	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.6856	930	2858	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	79.1567	982	2858	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	76.6949	647	2858	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	76.6757	688	2858	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	76.5601	671	2858	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	76.3309	596	2858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:49,464] [INFO] DFAST Taxonomy check result was written to GCF_006636205.1_ASM663620v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:49,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:49,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:49,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg369c2ea5-6156-4d95-8a31-7b9ec5131956/dqc_reference/checkm_data
[2024-01-24 14:54:49,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:49,542] [INFO] Task started: CheckM
[2024-01-24 14:54:49,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006636205.1_ASM663620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006636205.1_ASM663620v1_genomic.fna/checkm_input GCF_006636205.1_ASM663620v1_genomic.fna/checkm_result
[2024-01-24 14:57:04,355] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:04,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:04,384] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:04,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:04,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006636205.1_ASM663620v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:04,386] [INFO] Task started: Blastn
[2024-01-24 14:57:04,386] [INFO] Running command: blastn -query GCF_006636205.1_ASM663620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg369c2ea5-6156-4d95-8a31-7b9ec5131956/dqc_reference/reference_markers_gtdb.fasta -out GCF_006636205.1_ASM663620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:06,678] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:06,682] [INFO] Selected 12 target genomes.
[2024-01-24 14:57:06,683] [INFO] Target genome list was writen to GCF_006636205.1_ASM663620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:06,700] [INFO] Task started: fastANI
[2024-01-24 14:57:06,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e804b0b-9515-4e76-8913-cdfa1b2f141a/GCF_006636205.1_ASM663620v1_genomic.fna.gz --refList GCF_006636205.1_ASM663620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006636205.1_ASM663620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:36,792] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:36,810] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:36,810] [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_002846355.1	s__Kitasatospora sp002846355	96.054	2383	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.05	96.05	0.83	0.83	2	conclusive
GCF_007829815.1	s__Kitasatospora viridis	86.3213	1842	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744785.1	s__Kitasatospora azatica	85.9464	1616	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205575.1	s__Kitasatospora tateyamensis	85.4898	1473	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203855.1	s__Kitasatospora kifunensis	84.8824	1702	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424875.1	s__Kitasatospora sp001424875	82.5462	1320	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.95	99.95	0.99	0.99	2	-
GCF_014655955.1	s__Kitasatospora indigofera	82.425	1458	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716545.1	s__Kitasatospora phosalacinea	82.2533	1314	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	76.6765	689	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	76.5273	680	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308795.1	s__Nocardia thailandica	76.307	607	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737195.2	s__Sciscionella sp000737195	75.9547	451	2858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Sciscionella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:36,811] [INFO] GTDB search result was written to GCF_006636205.1_ASM663620v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:36,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:36,824] [INFO] DFAST_QC result json was written to GCF_006636205.1_ASM663620v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:36,825] [INFO] DFAST_QC completed!
[2024-01-24 14:57:36,825] [INFO] Total running time: 0h3m46s