[2024-01-24 14:39:29,359] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:29,361] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:29,361] [INFO] DQC Reference Directory: /var/lib/cwl/stgee9fd049-2fb3-4aad-968b-7ceac04fd539/dqc_reference
[2024-01-24 14:39:30,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:30,600] [INFO] Task started: Prodigal
[2024-01-24 14:39:30,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e1f6589-4b2b-4776-80b1-da1af23b3bc4/GCF_003258295.1_ASM325829v1_genomic.fna.gz | prodigal -d GCF_003258295.1_ASM325829v1_genomic.fna/cds.fna -a GCF_003258295.1_ASM325829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:52,254] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:52,254] [INFO] Task started: HMMsearch
[2024-01-24 14:39:52,254] [INFO] Running command: hmmsearch --tblout GCF_003258295.1_ASM325829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee9fd049-2fb3-4aad-968b-7ceac04fd539/dqc_reference/reference_markers.hmm GCF_003258295.1_ASM325829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:52,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:52,590] [INFO] Found 6/6 markers.
[2024-01-24 14:39:52,652] [INFO] Query marker FASTA was written to GCF_003258295.1_ASM325829v1_genomic.fna/markers.fasta
[2024-01-24 14:39:52,653] [INFO] Task started: Blastn
[2024-01-24 14:39:52,653] [INFO] Running command: blastn -query GCF_003258295.1_ASM325829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee9fd049-2fb3-4aad-968b-7ceac04fd539/dqc_reference/reference_markers.fasta -out GCF_003258295.1_ASM325829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:53,968] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:53,972] [INFO] Selected 13 target genomes.
[2024-01-24 14:39:53,972] [INFO] Target genome list was writen to GCF_003258295.1_ASM325829v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:53,977] [INFO] Task started: fastANI
[2024-01-24 14:39:53,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1f6589-4b2b-4776-80b1-da1af23b3bc4/GCF_003258295.1_ASM325829v1_genomic.fna.gz --refList GCF_003258295.1_ASM325829v1_genomic.fna/target_genomes.txt --output GCF_003258295.1_ASM325829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:20,835] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:20,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee9fd049-2fb3-4aad-968b-7ceac04fd539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:20,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee9fd049-2fb3-4aad-968b-7ceac04fd539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:20,846] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:20,846] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:20,847] [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
Streptacidiphilus pinicola	strain=MMS16-CNU450	GCA_003258295.1	2219663	2219663	type	True	100.0	2652	2662	95	conclusive
Streptacidiphilus neutrinimicus	strain=NBRC 100921	GCA_000787815.1	105420	105420	type	True	88.1807	1775	2662	95	below_threshold
Streptacidiphilus anmyonensis	strain=NBRC 103185	GCA_000787855.1	405782	405782	type	True	88.1369	1852	2662	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	88.094	1850	2662	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	87.483	1851	2662	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	87.4549	1863	2662	95	below_threshold
Streptacidiphilus fuscans	strain=NEAU-YB345	GCA_015690355.1	2789292	2789292	type	True	84.7944	1640	2662	95	below_threshold
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	81.1508	1322	2662	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	80.1125	1084	2662	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	79.7773	1154	2662	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	79.1631	925	2662	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	79.1446	926	2662	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	78.9362	884	2662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:20,848] [INFO] DFAST Taxonomy check result was written to GCF_003258295.1_ASM325829v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:20,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:20,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:20,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee9fd049-2fb3-4aad-968b-7ceac04fd539/dqc_reference/checkm_data
[2024-01-24 14:40:20,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:20,923] [INFO] Task started: CheckM
[2024-01-24 14:40:20,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258295.1_ASM325829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258295.1_ASM325829v1_genomic.fna/checkm_input GCF_003258295.1_ASM325829v1_genomic.fna/checkm_result
[2024-01-24 14:41:58,185] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:58,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:58,213] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:58,213] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:58,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258295.1_ASM325829v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:58,214] [INFO] Task started: Blastn
[2024-01-24 14:41:58,214] [INFO] Running command: blastn -query GCF_003258295.1_ASM325829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee9fd049-2fb3-4aad-968b-7ceac04fd539/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258295.1_ASM325829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:00,334] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:00,339] [INFO] Selected 8 target genomes.
[2024-01-24 14:42:00,339] [INFO] Target genome list was writen to GCF_003258295.1_ASM325829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:00,348] [INFO] Task started: fastANI
[2024-01-24 14:42:00,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1f6589-4b2b-4776-80b1-da1af23b3bc4/GCF_003258295.1_ASM325829v1_genomic.fna.gz --refList GCF_003258295.1_ASM325829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258295.1_ASM325829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:22,052] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:22,060] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:22,060] [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_003258295.1	s__Streptacidiphilus pinicola	100.0	2652	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000787855.1	s__Streptacidiphilus anmyonensis	88.1543	1850	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787815.1	s__Streptacidiphilus neutrinimicus	88.1541	1779	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787835.1	s__Streptacidiphilus melanogenes	88.1125	1847	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	87.4829	1858	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_015690355.1	s__Streptacidiphilus fuscans	84.8061	1639	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744705.1	s__Streptacidiphilus albus	81.1008	1346	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002943525.1	s__Kitasatospora sp002943525	80.094	1221	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:22,062] [INFO] GTDB search result was written to GCF_003258295.1_ASM325829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:22,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:22,068] [INFO] DFAST_QC result json was written to GCF_003258295.1_ASM325829v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:22,069] [INFO] DFAST_QC completed!
[2024-01-24 14:42:22,069] [INFO] Total running time: 0h2m53s