[2024-01-24 13:32:16,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:16,550] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:16,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg019f8205-e853-4380-ac67-70f0c36ce555/dqc_reference
[2024-01-24 13:32:17,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:17,904] [INFO] Task started: Prodigal
[2024-01-24 13:32:17,905] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb654424-ad74-4f50-9fb3-e284a921c4a3/GCF_000009765.2_ASM976v2_genomic.fna.gz | prodigal -d GCF_000009765.2_ASM976v2_genomic.fna/cds.fna -a GCF_000009765.2_ASM976v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:51,353] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:51,354] [INFO] Task started: HMMsearch
[2024-01-24 13:32:51,354] [INFO] Running command: hmmsearch --tblout GCF_000009765.2_ASM976v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg019f8205-e853-4380-ac67-70f0c36ce555/dqc_reference/reference_markers.hmm GCF_000009765.2_ASM976v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:51,748] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:51,750] [INFO] Found 6/6 markers.
[2024-01-24 13:32:51,824] [INFO] Query marker FASTA was written to GCF_000009765.2_ASM976v2_genomic.fna/markers.fasta
[2024-01-24 13:32:51,824] [INFO] Task started: Blastn
[2024-01-24 13:32:51,824] [INFO] Running command: blastn -query GCF_000009765.2_ASM976v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg019f8205-e853-4380-ac67-70f0c36ce555/dqc_reference/reference_markers.fasta -out GCF_000009765.2_ASM976v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:53,132] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:53,135] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:53,136] [INFO] Target genome list was writen to GCF_000009765.2_ASM976v2_genomic.fna/target_genomes.txt
[2024-01-24 13:32:53,141] [INFO] Task started: fastANI
[2024-01-24 13:32:53,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb654424-ad74-4f50-9fb3-e284a921c4a3/GCF_000009765.2_ASM976v2_genomic.fna.gz --refList GCF_000009765.2_ASM976v2_genomic.fna/target_genomes.txt --output GCF_000009765.2_ASM976v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:20,446] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:20,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg019f8205-e853-4380-ac67-70f0c36ce555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:20,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg019f8205-e853-4380-ac67-70f0c36ce555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:20,457] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:33:20,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:20,457] [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=MA-4680	GCA_000009765.2	33903	33903	type	True	100.0	3036	3039	95	conclusive
Streptomyces avermitilis	strain=NBRC 14893	GCA_000764715.1	33903	33903	type	True	99.9718	2981	3039	95	conclusive
Streptomyces avermitilis	strain=MA-4680	GCA_000968255.1	33903	33903	type	True	99.9676	2985	3039	95	conclusive
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	99.9625	3031	3039	95	conclusive
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	99.954	2889	3039	95	conclusive
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	85.0555	1720	3039	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.6827	1915	3039	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	84.591	1567	3039	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	84.2002	1856	3039	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	84.1056	1862	3039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:20,459] [INFO] DFAST Taxonomy check result was written to GCF_000009765.2_ASM976v2_genomic.fna/tc_result.tsv
[2024-01-24 13:33:20,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:20,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:20,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg019f8205-e853-4380-ac67-70f0c36ce555/dqc_reference/checkm_data
[2024-01-24 13:33:20,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:20,546] [INFO] Task started: CheckM
[2024-01-24 13:33:20,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000009765.2_ASM976v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000009765.2_ASM976v2_genomic.fna/checkm_input GCF_000009765.2_ASM976v2_genomic.fna/checkm_result
[2024-01-24 13:35:31,083] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:31,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:35:31,115] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:31,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:31,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000009765.2_ASM976v2_genomic.fna/markers.fasta)
[2024-01-24 13:35:31,116] [INFO] Task started: Blastn
[2024-01-24 13:35:31,116] [INFO] Running command: blastn -query GCF_000009765.2_ASM976v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg019f8205-e853-4380-ac67-70f0c36ce555/dqc_reference/reference_markers_gtdb.fasta -out GCF_000009765.2_ASM976v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:33,121] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:33,125] [INFO] Selected 23 target genomes.
[2024-01-24 13:35:33,125] [INFO] Target genome list was writen to GCF_000009765.2_ASM976v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:33,187] [INFO] Task started: fastANI
[2024-01-24 13:35:33,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb654424-ad74-4f50-9fb3-e284a921c4a3/GCF_000009765.2_ASM976v2_genomic.fna.gz --refList GCF_000009765.2_ASM976v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000009765.2_ASM976v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:29,673] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:29,698] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:29,698] [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	100.0	3038	3039	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	86.7454	2142	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_014650275.1	s__Streptomyces mirabilis	86.6711	2093	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	96.82	96.27	0.84	0.80	23	-
GCF_014645835.1	s__Streptomyces albiflavescens	86.5867	2039	3039	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	86.5402	2175	3039	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	86.5075	1791	3039	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	85.9199	1982	3039	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	85.761	1891	3039	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	85.5043	1910	3039	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	85.3149	1863	3039	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	85.2953	1940	3039	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	85.2233	1803	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
GCF_016598615.1	s__Streptomyces sp016598615	85.1894	1999	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725495.1	s__Streptomyces aureus_B	84.9621	1869	3039	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	84.8703	1728	3039	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	84.6865	1902	3039	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	84.6451	1922	3039	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	84.6218	1904	3039	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	84.4511	1867	3039	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	83.8984	1589	3039	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	83.3049	1576	3039	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	81.9514	1447	3039	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	81.7985	1351	3039	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 13:36:29,700] [INFO] GTDB search result was written to GCF_000009765.2_ASM976v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:29,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:29,705] [INFO] DFAST_QC result json was written to GCF_000009765.2_ASM976v2_genomic.fna/dqc_result.json
[2024-01-24 13:36:29,705] [INFO] DFAST_QC completed!
[2024-01-24 13:36:29,706] [INFO] Total running time: 0h4m13s