[2024-01-25 18:37:06,030] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:06,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:06,032] [INFO] DQC Reference Directory: /var/lib/cwl/stg44184feb-fb2a-42d2-970f-b29fb5169e6d/dqc_reference
[2024-01-25 18:37:07,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:07,189] [INFO] Task started: Prodigal
[2024-01-25 18:37:07,189] [INFO] Running command: gunzip -c /var/lib/cwl/stg41176bf8-d522-402a-a8e8-b13425bfdbf3/GCF_014646095.1_ASM1464609v1_genomic.fna.gz | prodigal -d GCF_014646095.1_ASM1464609v1_genomic.fna/cds.fna -a GCF_014646095.1_ASM1464609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:30,680] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:30,681] [INFO] Task started: HMMsearch
[2024-01-25 18:37:30,681] [INFO] Running command: hmmsearch --tblout GCF_014646095.1_ASM1464609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44184feb-fb2a-42d2-970f-b29fb5169e6d/dqc_reference/reference_markers.hmm GCF_014646095.1_ASM1464609v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:30,991] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:30,992] [INFO] Found 6/6 markers.
[2024-01-25 18:37:31,058] [INFO] Query marker FASTA was written to GCF_014646095.1_ASM1464609v1_genomic.fna/markers.fasta
[2024-01-25 18:37:31,058] [INFO] Task started: Blastn
[2024-01-25 18:37:31,058] [INFO] Running command: blastn -query GCF_014646095.1_ASM1464609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44184feb-fb2a-42d2-970f-b29fb5169e6d/dqc_reference/reference_markers.fasta -out GCF_014646095.1_ASM1464609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:32,249] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:32,256] [INFO] Selected 19 target genomes.
[2024-01-25 18:37:32,256] [INFO] Target genome list was writen to GCF_014646095.1_ASM1464609v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:32,308] [INFO] Task started: fastANI
[2024-01-25 18:37:32,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg41176bf8-d522-402a-a8e8-b13425bfdbf3/GCF_014646095.1_ASM1464609v1_genomic.fna.gz --refList GCF_014646095.1_ASM1464609v1_genomic.fna/target_genomes.txt --output GCF_014646095.1_ASM1464609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:38:12,852] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:12,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44184feb-fb2a-42d2-970f-b29fb5169e6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:38:12,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44184feb-fb2a-42d2-970f-b29fb5169e6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:38:12,866] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:38:12,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:38:12,866] [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 lacrimifluminis	strain=CGMCC 4.7272	GCA_014646095.1	1500077	1500077	type	True	100.0	2947	2949	95	conclusive
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	89.7759	2027	2949	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.6238	1919	2949	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.4701	1655	2949	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.4505	1754	2949	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.3859	1620	2949	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	84.3034	1759	2949	95	below_threshold
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	84.299	1831	2949	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.2866	1813	2949	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	84.2165	1959	2949	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	84.009	1914	2949	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.9728	1744	2949	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.9546	1911	2949	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	83.6902	1643	2949	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	83.6639	1617	2949	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	83.3906	1616	2949	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	82.3093	1224	2949	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	82.2246	1408	2949	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.2225	1291	2949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:38:12,867] [INFO] DFAST Taxonomy check result was written to GCF_014646095.1_ASM1464609v1_genomic.fna/tc_result.tsv
[2024-01-25 18:38:12,868] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:38:12,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:38:12,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44184feb-fb2a-42d2-970f-b29fb5169e6d/dqc_reference/checkm_data
[2024-01-25 18:38:12,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:38:12,950] [INFO] Task started: CheckM
[2024-01-25 18:38:12,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646095.1_ASM1464609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646095.1_ASM1464609v1_genomic.fna/checkm_input GCF_014646095.1_ASM1464609v1_genomic.fna/checkm_result
[2024-01-25 18:39:52,987] [INFO] Task succeeded: CheckM
[2024-01-25 18:39:52,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-25 18:39:53,011] [INFO] ===== Completeness check finished =====
[2024-01-25 18:39:53,011] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:39:53,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646095.1_ASM1464609v1_genomic.fna/markers.fasta)
[2024-01-25 18:39:53,012] [INFO] Task started: Blastn
[2024-01-25 18:39:53,012] [INFO] Running command: blastn -query GCF_014646095.1_ASM1464609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44184feb-fb2a-42d2-970f-b29fb5169e6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646095.1_ASM1464609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:55,012] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:55,045] [INFO] Selected 6 target genomes.
[2024-01-25 18:39:55,045] [INFO] Target genome list was writen to GCF_014646095.1_ASM1464609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:39:55,050] [INFO] Task started: fastANI
[2024-01-25 18:39:55,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg41176bf8-d522-402a-a8e8-b13425bfdbf3/GCF_014646095.1_ASM1464609v1_genomic.fna.gz --refList GCF_014646095.1_ASM1464609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646095.1_ASM1464609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:10,244] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:10,249] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:10,250] [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_014646095.1	s__Streptomyces lacrimifluminis	100.0	2947	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010548275.1	s__Streptomyces sp010548275	93.0257	2321	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331005.1	s__Streptomyces turgidiscabies	91.3121	1999	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.67	0.92	0.88	3	-
GCF_001280005.1	s__Streptomyces sp001280005	90.7755	2037	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418565.1	s__Streptomyces graminilatus	90.697	1715	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954775.1	s__Streptomyces geranii	89.7736	2027	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:10,251] [INFO] GTDB search result was written to GCF_014646095.1_ASM1464609v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:10,252] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:10,254] [INFO] DFAST_QC result json was written to GCF_014646095.1_ASM1464609v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:10,254] [INFO] DFAST_QC completed!
[2024-01-25 18:40:10,255] [INFO] Total running time: 0h3m4s