[2024-01-24 11:05:25,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,307] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,307] [INFO] DQC Reference Directory: /var/lib/cwl/stgf79f2244-2101-4c94-b837-609acc5d7f1e/dqc_reference
[2024-01-24 11:05:26,729] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,730] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,731] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8a02257-adf2-41f6-8a4b-832f2f82cdeb/GCF_014648995.1_ASM1464899v1_genomic.fna.gz | prodigal -d GCF_014648995.1_ASM1464899v1_genomic.fna/cds.fna -a GCF_014648995.1_ASM1464899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:51,961] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:51,962] [INFO] Task started: HMMsearch
[2024-01-24 11:05:51,962] [INFO] Running command: hmmsearch --tblout GCF_014648995.1_ASM1464899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf79f2244-2101-4c94-b837-609acc5d7f1e/dqc_reference/reference_markers.hmm GCF_014648995.1_ASM1464899v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:52,339] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:52,340] [INFO] Found 6/6 markers.
[2024-01-24 11:05:52,410] [INFO] Query marker FASTA was written to GCF_014648995.1_ASM1464899v1_genomic.fna/markers.fasta
[2024-01-24 11:05:52,410] [INFO] Task started: Blastn
[2024-01-24 11:05:52,410] [INFO] Running command: blastn -query GCF_014648995.1_ASM1464899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf79f2244-2101-4c94-b837-609acc5d7f1e/dqc_reference/reference_markers.fasta -out GCF_014648995.1_ASM1464899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:53,727] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:53,730] [INFO] Selected 15 target genomes.
[2024-01-24 11:05:53,731] [INFO] Target genome list was writen to GCF_014648995.1_ASM1464899v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:53,735] [INFO] Task started: fastANI
[2024-01-24 11:05:53,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8a02257-adf2-41f6-8a4b-832f2f82cdeb/GCF_014648995.1_ASM1464899v1_genomic.fna.gz --refList GCF_014648995.1_ASM1464899v1_genomic.fna/target_genomes.txt --output GCF_014648995.1_ASM1464899v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:28,603] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:28,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf79f2244-2101-4c94-b837-609acc5d7f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:28,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf79f2244-2101-4c94-b837-609acc5d7f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:28,619] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:28,619] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:06:28,619] [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 massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	100.0	2984	2987	95	inconclusive
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	95.2048	2207	2987	95	inconclusive
Streptomyces luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	94.7892	2451	2987	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	93.1506	2421	2987	95	below_threshold
Streptomyces hawaiiensis	strain=ATCC 12236	GCA_004803895.1	67305	67305	type	True	93.0946	2343	2987	95	below_threshold
Streptomyces flavovariabilis	strain=NRRL B-16367	GCA_000725785.1	284031	284031	type	True	92.9221	2337	2987	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	92.7241	2316	2987	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	92.7079	2376	2987	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	92.7078	2376	2987	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	92.2384	1864	2987	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	92.1007	2043	2987	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	90.9939	2236	2987	95	below_threshold
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	90.8458	2354	2987	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.8258	2334	2987	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.8289	1810	2987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:28,621] [INFO] DFAST Taxonomy check result was written to GCF_014648995.1_ASM1464899v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:28,622] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:28,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:28,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf79f2244-2101-4c94-b837-609acc5d7f1e/dqc_reference/checkm_data
[2024-01-24 11:06:28,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:28,702] [INFO] Task started: CheckM
[2024-01-24 11:06:28,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648995.1_ASM1464899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648995.1_ASM1464899v1_genomic.fna/checkm_input GCF_014648995.1_ASM1464899v1_genomic.fna/checkm_result
[2024-01-24 11:08:34,182] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:34,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:34,212] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:34,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:34,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648995.1_ASM1464899v1_genomic.fna/markers.fasta)
[2024-01-24 11:08:34,213] [INFO] Task started: Blastn
[2024-01-24 11:08:34,213] [INFO] Running command: blastn -query GCF_014648995.1_ASM1464899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf79f2244-2101-4c94-b837-609acc5d7f1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648995.1_ASM1464899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:36,264] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:36,267] [INFO] Selected 9 target genomes.
[2024-01-24 11:08:36,268] [INFO] Target genome list was writen to GCF_014648995.1_ASM1464899v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:36,287] [INFO] Task started: fastANI
[2024-01-24 11:08:36,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8a02257-adf2-41f6-8a4b-832f2f82cdeb/GCF_014648995.1_ASM1464899v1_genomic.fna.gz --refList GCF_014648995.1_ASM1464899v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648995.1_ASM1464899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:57,858] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:57,873] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:57,873] [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_014648995.1	s__Streptomyces massasporeus	100.0	2984	2987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	conclusive
GCF_014205055.1	s__Streptomyces luteogriseus	94.7781	2452	2987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCA_014204745.1	s__Streptomyces collinus	93.1173	2404	2987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_004803895.1	s__Streptomyces hawaiiensis	93.0787	2345	2987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCF_014202475.1	s__Streptomyces paradoxus	92.9425	2389	2987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611795.1	s__Streptomyces qaidamensis	92.7581	2374	2987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_000717055.1	s__Streptomyces iakyrus	92.732	2315	2987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_007655005.1	s__Streptomyces tibetensis	92.7309	2373	2987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001280065.1	s__Streptomyces sp001280065	92.0661	2241	2987	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 11:08:57,874] [INFO] GTDB search result was written to GCF_014648995.1_ASM1464899v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:57,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:57,878] [INFO] DFAST_QC result json was written to GCF_014648995.1_ASM1464899v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:57,879] [INFO] DFAST_QC completed!
[2024-01-24 11:08:57,879] [INFO] Total running time: 0h3m33s