[2024-01-25 18:09:50,709] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:50,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:50,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ad3e204-7839-4fa4-a0a1-1f4ffe613c84/dqc_reference
[2024-01-25 18:09:51,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:51,865] [INFO] Task started: Prodigal
[2024-01-25 18:09:51,865] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2fde459-1140-45a4-a708-a41fa865ad3c/GCF_003265665.1_ASM326566v1_genomic.fna.gz | prodigal -d GCF_003265665.1_ASM326566v1_genomic.fna/cds.fna -a GCF_003265665.1_ASM326566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:10,203] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:10,203] [INFO] Task started: HMMsearch
[2024-01-25 18:10:10,203] [INFO] Running command: hmmsearch --tblout GCF_003265665.1_ASM326566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ad3e204-7839-4fa4-a0a1-1f4ffe613c84/dqc_reference/reference_markers.hmm GCF_003265665.1_ASM326566v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:10,495] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:10,496] [INFO] Found 6/6 markers.
[2024-01-25 18:10:10,547] [INFO] Query marker FASTA was written to GCF_003265665.1_ASM326566v1_genomic.fna/markers.fasta
[2024-01-25 18:10:10,547] [INFO] Task started: Blastn
[2024-01-25 18:10:10,547] [INFO] Running command: blastn -query GCF_003265665.1_ASM326566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ad3e204-7839-4fa4-a0a1-1f4ffe613c84/dqc_reference/reference_markers.fasta -out GCF_003265665.1_ASM326566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:11,803] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:11,807] [INFO] Selected 11 target genomes.
[2024-01-25 18:10:11,808] [INFO] Target genome list was writen to GCF_003265665.1_ASM326566v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:11,816] [INFO] Task started: fastANI
[2024-01-25 18:10:11,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2fde459-1140-45a4-a708-a41fa865ad3c/GCF_003265665.1_ASM326566v1_genomic.fna.gz --refList GCF_003265665.1_ASM326566v1_genomic.fna/target_genomes.txt --output GCF_003265665.1_ASM326566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:34,709] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:34,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ad3e204-7839-4fa4-a0a1-1f4ffe613c84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:34,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ad3e204-7839-4fa4-a0a1-1f4ffe613c84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:34,720] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:10:34,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:34,720] [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 qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	100.0	2371	2373	95	conclusive
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	99.9842	2352	2373	95	conclusive
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	87.5105	1757	2373	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	87.0459	1723	2373	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	86.9651	1611	2373	95	below_threshold
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	84.6843	1597	2373	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.2418	1202	2373	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.1976	908	2373	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.1462	1199	2373	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	79.9921	1215	2373	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.8652	1269	2373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:34,721] [INFO] DFAST Taxonomy check result was written to GCF_003265665.1_ASM326566v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:34,721] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:34,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:34,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ad3e204-7839-4fa4-a0a1-1f4ffe613c84/dqc_reference/checkm_data
[2024-01-25 18:10:34,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:34,799] [INFO] Task started: CheckM
[2024-01-25 18:10:34,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003265665.1_ASM326566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003265665.1_ASM326566v1_genomic.fna/checkm_input GCF_003265665.1_ASM326566v1_genomic.fna/checkm_result
[2024-01-25 18:12:25,588] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:25,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:25,609] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:25,609] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:25,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003265665.1_ASM326566v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:25,610] [INFO] Task started: Blastn
[2024-01-25 18:12:25,610] [INFO] Running command: blastn -query GCF_003265665.1_ASM326566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ad3e204-7839-4fa4-a0a1-1f4ffe613c84/dqc_reference/reference_markers_gtdb.fasta -out GCF_003265665.1_ASM326566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:27,680] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:27,683] [INFO] Selected 7 target genomes.
[2024-01-25 18:12:27,683] [INFO] Target genome list was writen to GCF_003265665.1_ASM326566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:27,699] [INFO] Task started: fastANI
[2024-01-25 18:12:27,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2fde459-1140-45a4-a708-a41fa865ad3c/GCF_003265665.1_ASM326566v1_genomic.fna.gz --refList GCF_003265665.1_ASM326566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003265665.1_ASM326566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:42,173] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:42,179] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:42,179] [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_900111245.1	s__Streptomyces qinglanensis	99.9842	2352	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000424765.1	s__Streptomyces sp000424765	94.5182	2055	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_017676345.1	s__Streptomyces smyrnaeus	87.5044	1758	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_017676385.1	s__Streptomyces sp017676385	87.0148	1728	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676365.1	s__Streptomyces oryzae	86.9729	1609	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	85.2831	1611	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323735.1	s__Streptomyces reniochalinae	84.649	1602	2373	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 18:12:42,180] [INFO] GTDB search result was written to GCF_003265665.1_ASM326566v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:42,181] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:42,183] [INFO] DFAST_QC result json was written to GCF_003265665.1_ASM326566v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:42,183] [INFO] DFAST_QC completed!
[2024-01-25 18:12:42,183] [INFO] Total running time: 0h2m51s