[2024-01-24 15:18:19,561] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg96ddd274-c655-4d02-8399-355709e33d85/dqc_reference
[2024-01-24 15:18:20,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,818] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb26d266-99bb-4c88-82b0-5a1e042be222/GCF_016411765.1_ASM1641176v1_genomic.fna.gz | prodigal -d GCF_016411765.1_ASM1641176v1_genomic.fna/cds.fna -a GCF_016411765.1_ASM1641176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:54,448] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:54,448] [INFO] Task started: HMMsearch
[2024-01-24 15:18:54,449] [INFO] Running command: hmmsearch --tblout GCF_016411765.1_ASM1641176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96ddd274-c655-4d02-8399-355709e33d85/dqc_reference/reference_markers.hmm GCF_016411765.1_ASM1641176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:54,879] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:54,880] [INFO] Found 6/6 markers.
[2024-01-24 15:18:54,960] [INFO] Query marker FASTA was written to GCF_016411765.1_ASM1641176v1_genomic.fna/markers.fasta
[2024-01-24 15:18:54,960] [INFO] Task started: Blastn
[2024-01-24 15:18:54,960] [INFO] Running command: blastn -query GCF_016411765.1_ASM1641176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96ddd274-c655-4d02-8399-355709e33d85/dqc_reference/reference_markers.fasta -out GCF_016411765.1_ASM1641176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:56,344] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:56,347] [INFO] Selected 12 target genomes.
[2024-01-24 15:18:56,348] [INFO] Target genome list was writen to GCF_016411765.1_ASM1641176v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:56,353] [INFO] Task started: fastANI
[2024-01-24 15:18:56,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb26d266-99bb-4c88-82b0-5a1e042be222/GCF_016411765.1_ASM1641176v1_genomic.fna.gz --refList GCF_016411765.1_ASM1641176v1_genomic.fna/target_genomes.txt --output GCF_016411765.1_ASM1641176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:31,751] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:31,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96ddd274-c655-4d02-8399-355709e33d85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:31,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96ddd274-c655-4d02-8399-355709e33d85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:31,765] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:31,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:31,766] [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 flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	100.0	3158	3194	95	conclusive
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	99.9756	3041	3194	95	conclusive
Streptomyces alboflavus	strain=NRRL B-2373	GCA_000716675.1	67267	67267	type	True	92.5088	2608	3194	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	89.8119	2469	3194	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	89.676	2387	3194	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	86.5876	2288	3194	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	84.3743	2000	3194	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	84.1831	1752	3194	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	84.1507	1811	3194	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	82.3162	1576	3194	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	82.1034	1453	3194	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	81.1382	1561	3194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:31,767] [INFO] DFAST Taxonomy check result was written to GCF_016411765.1_ASM1641176v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:31,768] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:31,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:31,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96ddd274-c655-4d02-8399-355709e33d85/dqc_reference/checkm_data
[2024-01-24 15:19:31,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:31,855] [INFO] Task started: CheckM
[2024-01-24 15:19:31,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016411765.1_ASM1641176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016411765.1_ASM1641176v1_genomic.fna/checkm_input GCF_016411765.1_ASM1641176v1_genomic.fna/checkm_result
[2024-01-24 15:21:28,943] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:28,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:28,973] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:28,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:28,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016411765.1_ASM1641176v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:28,974] [INFO] Task started: Blastn
[2024-01-24 15:21:28,974] [INFO] Running command: blastn -query GCF_016411765.1_ASM1641176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96ddd274-c655-4d02-8399-355709e33d85/dqc_reference/reference_markers_gtdb.fasta -out GCF_016411765.1_ASM1641176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:31,173] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:31,177] [INFO] Selected 7 target genomes.
[2024-01-24 15:21:31,177] [INFO] Target genome list was writen to GCF_016411765.1_ASM1641176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:31,206] [INFO] Task started: fastANI
[2024-01-24 15:21:31,206] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb26d266-99bb-4c88-82b0-5a1e042be222/GCF_016411765.1_ASM1641176v1_genomic.fna.gz --refList GCF_016411765.1_ASM1641176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016411765.1_ASM1641176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:52,647] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:52,654] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:52,655] [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_014650815.1	s__Streptomyces flavofungini	99.9756	3041	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000716675.1	s__Streptomyces alboflavus	92.5408	2603	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
GCF_014646335.1	s__Streptomyces lasiicapitis	89.848	2461	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.86	0.95	0.95	2	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	89.7273	2114	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	89.6785	2387	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755605.1	s__Streptomyces typhae	87.8836	2254	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.66	98.66	0.93	0.93	2	-
GCF_004127445.1	s__Streptomyces alfalfae	84.2022	1806	3194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:52,656] [INFO] GTDB search result was written to GCF_016411765.1_ASM1641176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:52,657] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:52,660] [INFO] DFAST_QC result json was written to GCF_016411765.1_ASM1641176v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:52,660] [INFO] DFAST_QC completed!
[2024-01-24 15:21:52,661] [INFO] Total running time: 0h3m33s