[2024-01-24 13:01:53,272] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:53,274] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:53,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg2314e43c-0de0-48d2-b887-c5e8933a3b65/dqc_reference
[2024-01-24 13:01:54,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,569] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,569] [INFO] Running command: gunzip -c /var/lib/cwl/stga4f07034-d387-499c-99dc-c0d6b51cf2fb/GCF_003014735.1_ASM301473v1_genomic.fna.gz | prodigal -d GCF_003014735.1_ASM301473v1_genomic.fna/cds.fna -a GCF_003014735.1_ASM301473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:28,440] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:28,441] [INFO] Task started: HMMsearch
[2024-01-24 13:02:28,441] [INFO] Running command: hmmsearch --tblout GCF_003014735.1_ASM301473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2314e43c-0de0-48d2-b887-c5e8933a3b65/dqc_reference/reference_markers.hmm GCF_003014735.1_ASM301473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:28,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:28,955] [INFO] Found 6/6 markers.
[2024-01-24 13:02:29,027] [INFO] Query marker FASTA was written to GCF_003014735.1_ASM301473v1_genomic.fna/markers.fasta
[2024-01-24 13:02:29,027] [INFO] Task started: Blastn
[2024-01-24 13:02:29,027] [INFO] Running command: blastn -query GCF_003014735.1_ASM301473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2314e43c-0de0-48d2-b887-c5e8933a3b65/dqc_reference/reference_markers.fasta -out GCF_003014735.1_ASM301473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:30,360] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:30,366] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:30,367] [INFO] Target genome list was writen to GCF_003014735.1_ASM301473v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:30,373] [INFO] Task started: fastANI
[2024-01-24 13:02:30,373] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f07034-d387-499c-99dc-c0d6b51cf2fb/GCF_003014735.1_ASM301473v1_genomic.fna.gz --refList GCF_003014735.1_ASM301473v1_genomic.fna/target_genomes.txt --output GCF_003014735.1_ASM301473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:04,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:04,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2314e43c-0de0-48d2-b887-c5e8933a3b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:04,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2314e43c-0de0-48d2-b887-c5e8933a3b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:04,105] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:03:04,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:03:04,106] [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
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	100.0	2950	2953	95	conclusive
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	90.4745	2232	2953	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	90.3897	2236	2953	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	88.3295	2089	2953	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	87.8445	2081	2953	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	84.9845	2075	2953	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	83.7949	1524	2953	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	83.7599	1606	2953	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	83.5731	1732	2953	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	83.2184	1556	2953	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	80.1582	1382	2953	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.9269	1010	2953	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.1494	933	2953	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.9955	1185	2953	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:04,108] [INFO] DFAST Taxonomy check result was written to GCF_003014735.1_ASM301473v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:04,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:04,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:04,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2314e43c-0de0-48d2-b887-c5e8933a3b65/dqc_reference/checkm_data
[2024-01-24 13:03:04,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:04,190] [INFO] Task started: CheckM
[2024-01-24 13:03:04,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014735.1_ASM301473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014735.1_ASM301473v1_genomic.fna/checkm_input GCF_003014735.1_ASM301473v1_genomic.fna/checkm_result
[2024-01-24 13:05:30,421] [INFO] Task succeeded: CheckM
[2024-01-24 13:05:30,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:05:30,452] [INFO] ===== Completeness check finished =====
[2024-01-24 13:05:30,453] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:05:30,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014735.1_ASM301473v1_genomic.fna/markers.fasta)
[2024-01-24 13:05:30,453] [INFO] Task started: Blastn
[2024-01-24 13:05:30,454] [INFO] Running command: blastn -query GCF_003014735.1_ASM301473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2314e43c-0de0-48d2-b887-c5e8933a3b65/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014735.1_ASM301473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:05:32,513] [INFO] Task succeeded: Blastn
[2024-01-24 13:05:32,518] [INFO] Selected 11 target genomes.
[2024-01-24 13:05:32,518] [INFO] Target genome list was writen to GCF_003014735.1_ASM301473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:05:32,593] [INFO] Task started: fastANI
[2024-01-24 13:05:32,594] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f07034-d387-499c-99dc-c0d6b51cf2fb/GCF_003014735.1_ASM301473v1_genomic.fna.gz --refList GCF_003014735.1_ASM301473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014735.1_ASM301473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:06:01,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:06:02,016] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:06:02,016] [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_003014735.1	s__Actinosynnema carneum	100.0	2950	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	conclusive
GCF_001280085.1	s__Actinosynnema sp001280085	90.9084	2294	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	90.5157	2226	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_006716745.1	s__Actinosynnema saharense	90.4	2235	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	88.3147	2093	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716595.1	s__Actinosynnema sp000716595	88.0416	2057	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984175.1	s__Actinosynnema sp001984175	87.9357	2019	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205015.1	s__Actinosynnema ecbatanense	87.8481	2081	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	83.8315	1519	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	83.7239	1613	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328705.1	s__Actinosynnema espanaense	83.5255	1741	2953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:06:02,018] [INFO] GTDB search result was written to GCF_003014735.1_ASM301473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:06:02,019] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:06:02,023] [INFO] DFAST_QC result json was written to GCF_003014735.1_ASM301473v1_genomic.fna/dqc_result.json
[2024-01-24 13:06:02,023] [INFO] DFAST_QC completed!
[2024-01-24 13:06:02,023] [INFO] Total running time: 0h4m9s