[2024-01-24 14:32:33,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:33,936] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:33,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg23599c7e-b950-4bf1-8577-e3e4e2304184/dqc_reference
[2024-01-24 14:32:35,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:35,425] [INFO] Task started: Prodigal
[2024-01-24 14:32:35,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg0382df32-fa63-4964-8af2-322b20c22b6c/GCF_005405965.1_ASM540596v1_genomic.fna.gz | prodigal -d GCF_005405965.1_ASM540596v1_genomic.fna/cds.fna -a GCF_005405965.1_ASM540596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:33:07,732] [INFO] Task succeeded: Prodigal
[2024-01-24 14:33:07,733] [INFO] Task started: HMMsearch
[2024-01-24 14:33:07,733] [INFO] Running command: hmmsearch --tblout GCF_005405965.1_ASM540596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23599c7e-b950-4bf1-8577-e3e4e2304184/dqc_reference/reference_markers.hmm GCF_005405965.1_ASM540596v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:33:08,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:33:08,116] [INFO] Found 6/6 markers.
[2024-01-24 14:33:08,203] [INFO] Query marker FASTA was written to GCF_005405965.1_ASM540596v1_genomic.fna/markers.fasta
[2024-01-24 14:33:08,203] [INFO] Task started: Blastn
[2024-01-24 14:33:08,203] [INFO] Running command: blastn -query GCF_005405965.1_ASM540596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23599c7e-b950-4bf1-8577-e3e4e2304184/dqc_reference/reference_markers.fasta -out GCF_005405965.1_ASM540596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:09,614] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:09,618] [INFO] Selected 10 target genomes.
[2024-01-24 14:33:09,619] [INFO] Target genome list was writen to GCF_005405965.1_ASM540596v1_genomic.fna/target_genomes.txt
[2024-01-24 14:33:09,628] [INFO] Task started: fastANI
[2024-01-24 14:33:09,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg0382df32-fa63-4964-8af2-322b20c22b6c/GCF_005405965.1_ASM540596v1_genomic.fna.gz --refList GCF_005405965.1_ASM540596v1_genomic.fna/target_genomes.txt --output GCF_005405965.1_ASM540596v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:33:34,996] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:34,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23599c7e-b950-4bf1-8577-e3e4e2304184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:33:34,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23599c7e-b950-4bf1-8577-e3e4e2304184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:33:35,012] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:33:35,012] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:33:35,013] [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 avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	100.0	3489	3491	95	conclusive
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	99.9718	3027	3491	95	conclusive
Streptomyces avermitilis	strain=NBRC 14893	GCA_000764715.1	33903	33903	type	True	99.962	3416	3491	95	conclusive
Streptomyces avermitilis	strain=MA-4680	GCA_000968255.1	33903	33903	type	True	99.9579	3429	3491	95	conclusive
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	99.95	2939	3491	95	conclusive
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	84.9446	1773	3491	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	84.2849	1634	3491	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	84.0398	1930	3491	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.8645	1950	3491	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	82.4642	1671	3491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:33:35,014] [INFO] DFAST Taxonomy check result was written to GCF_005405965.1_ASM540596v1_genomic.fna/tc_result.tsv
[2024-01-24 14:33:35,015] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:33:35,015] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:33:35,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23599c7e-b950-4bf1-8577-e3e4e2304184/dqc_reference/checkm_data
[2024-01-24 14:33:35,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:33:35,112] [INFO] Task started: CheckM
[2024-01-24 14:33:35,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405965.1_ASM540596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405965.1_ASM540596v1_genomic.fna/checkm_input GCF_005405965.1_ASM540596v1_genomic.fna/checkm_result
[2024-01-24 14:35:50,497] [INFO] Task succeeded: CheckM
[2024-01-24 14:35:50,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:35:50,530] [INFO] ===== Completeness check finished =====
[2024-01-24 14:35:50,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:35:50,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405965.1_ASM540596v1_genomic.fna/markers.fasta)
[2024-01-24 14:35:50,531] [INFO] Task started: Blastn
[2024-01-24 14:35:50,531] [INFO] Running command: blastn -query GCF_005405965.1_ASM540596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23599c7e-b950-4bf1-8577-e3e4e2304184/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405965.1_ASM540596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:35:52,988] [INFO] Task succeeded: Blastn
[2024-01-24 14:35:52,994] [INFO] Selected 22 target genomes.
[2024-01-24 14:35:52,994] [INFO] Target genome list was writen to GCF_005405965.1_ASM540596v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:35:53,124] [INFO] Task started: fastANI
[2024-01-24 14:35:53,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg0382df32-fa63-4964-8af2-322b20c22b6c/GCF_005405965.1_ASM540596v1_genomic.fna.gz --refList GCF_005405965.1_ASM540596v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405965.1_ASM540596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:36:49,237] [INFO] Task succeeded: fastANI
[2024-01-24 14:36:49,260] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:36:49,260] [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_000009765.2	s__Streptomyces avermitilis	99.9717	3028	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.91	0.98	0.92	9	conclusive
GCF_001514115.1	s__Streptomyces olivochromogenes	86.4938	2298	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_014645835.1	s__Streptomyces albiflavescens	86.4931	2146	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012273535.1	s__Streptomyces sp002846625	86.3515	2326	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4492	97.43	96.23	0.83	0.78	4	-
GCF_002946835.1	s__Streptomyces dengpaensis	86.2954	1854	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	1.00	1.00	2	-
GCF_012273515.1	s__Streptomyces sp012273515	85.8032	2073	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664315.1	s__Streptomyces sp003664315	85.5703	1961	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746395.1	s__Streptomyces mirabilis_A	85.3073	2009	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078175.1	s__Streptomyces sp002078175	85.1586	1932	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.16	97.16	0.90	0.90	2	-
GCF_008905045.1	s__Streptomyces albicerus	85.1374	2022	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	85.0734	2095	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911015.1	s__Streptomyces populi	84.9791	1909	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
GCF_000725495.1	s__Streptomyces aureus_B	84.8242	1924	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369065.1	s__Streptomyces sp008369065	84.6246	1804	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163075.1	s__Streptomyces sp015163075	84.5731	1975	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	84.5577	1943	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514065.1	s__Streptomyces antibioticus	84.4984	1952	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	N/A	N/A	N/A	N/A	1	-
GCF_000367365.1	s__Streptomyces prunicolor	84.2275	1963	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112575.1	s__Streptomyces ardesiacus	83.625	1646	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_003945545.1	s__Streptomyces sp003945545	83.2012	1620	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054555.1	s__Streptomyces lunaelactis	81.9537	1494	3491	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.21	97.91	0.90	0.85	18	-
GCF_018614585.1	s__Streptomyces sp018614585	81.7628	1389	3491	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 14:36:49,262] [INFO] GTDB search result was written to GCF_005405965.1_ASM540596v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:36:49,263] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:36:49,267] [INFO] DFAST_QC result json was written to GCF_005405965.1_ASM540596v1_genomic.fna/dqc_result.json
[2024-01-24 14:36:49,267] [INFO] DFAST_QC completed!
[2024-01-24 14:36:49,268] [INFO] Total running time: 0h4m15s