[2024-01-25 17:46:50,526] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:50,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:50,528] [INFO] DQC Reference Directory: /var/lib/cwl/stgaabe8fb5-a371-4659-9ef9-dd97bdab002e/dqc_reference
[2024-01-25 17:46:51,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:51,644] [INFO] Task started: Prodigal
[2024-01-25 17:46:51,644] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb89f1bc-e30e-4341-8369-7e0e74365e75/GCF_014203665.1_ASM1420366v1_genomic.fna.gz | prodigal -d GCF_014203665.1_ASM1420366v1_genomic.fna/cds.fna -a GCF_014203665.1_ASM1420366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:16,170] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:16,171] [INFO] Task started: HMMsearch
[2024-01-25 17:47:16,171] [INFO] Running command: hmmsearch --tblout GCF_014203665.1_ASM1420366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaabe8fb5-a371-4659-9ef9-dd97bdab002e/dqc_reference/reference_markers.hmm GCF_014203665.1_ASM1420366v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:16,497] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:16,498] [INFO] Found 6/6 markers.
[2024-01-25 17:47:16,566] [INFO] Query marker FASTA was written to GCF_014203665.1_ASM1420366v1_genomic.fna/markers.fasta
[2024-01-25 17:47:16,566] [INFO] Task started: Blastn
[2024-01-25 17:47:16,566] [INFO] Running command: blastn -query GCF_014203665.1_ASM1420366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaabe8fb5-a371-4659-9ef9-dd97bdab002e/dqc_reference/reference_markers.fasta -out GCF_014203665.1_ASM1420366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:17,951] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:17,954] [INFO] Selected 15 target genomes.
[2024-01-25 17:47:17,954] [INFO] Target genome list was writen to GCF_014203665.1_ASM1420366v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:17,965] [INFO] Task started: fastANI
[2024-01-25 17:47:17,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb89f1bc-e30e-4341-8369-7e0e74365e75/GCF_014203665.1_ASM1420366v1_genomic.fna.gz --refList GCF_014203665.1_ASM1420366v1_genomic.fna/target_genomes.txt --output GCF_014203665.1_ASM1420366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:51,835] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:51,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaabe8fb5-a371-4659-9ef9-dd97bdab002e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:51,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaabe8fb5-a371-4659-9ef9-dd97bdab002e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:51,845] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:47:51,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:51,845] [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 tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	100.0	2665	2667	95	conclusive
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	87.0944	1742	2667	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	86.9751	1805	2667	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	86.5338	2023	2667	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	84.9306	1694	2667	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	84.799	1736	2667	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	84.1931	1620	2667	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	84.1644	1633	2667	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	84.0531	1675	2667	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	83.3347	1693	2667	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	83.2438	1734	2667	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.462	1262	2667	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	80.0164	1200	2667	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.2496	840	2667	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.8588	599	2667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:51,847] [INFO] DFAST Taxonomy check result was written to GCF_014203665.1_ASM1420366v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:51,847] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:51,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:51,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaabe8fb5-a371-4659-9ef9-dd97bdab002e/dqc_reference/checkm_data
[2024-01-25 17:47:51,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:51,920] [INFO] Task started: CheckM
[2024-01-25 17:47:51,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203665.1_ASM1420366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203665.1_ASM1420366v1_genomic.fna/checkm_input GCF_014203665.1_ASM1420366v1_genomic.fna/checkm_result
[2024-01-25 17:50:00,590] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:00,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:00,618] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:00,619] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:00,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203665.1_ASM1420366v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:00,620] [INFO] Task started: Blastn
[2024-01-25 17:50:00,620] [INFO] Running command: blastn -query GCF_014203665.1_ASM1420366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaabe8fb5-a371-4659-9ef9-dd97bdab002e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203665.1_ASM1420366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:02,785] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:02,790] [INFO] Selected 11 target genomes.
[2024-01-25 17:50:02,790] [INFO] Target genome list was writen to GCF_014203665.1_ASM1420366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:02,799] [INFO] Task started: fastANI
[2024-01-25 17:50:02,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb89f1bc-e30e-4341-8369-7e0e74365e75/GCF_014203665.1_ASM1420366v1_genomic.fna.gz --refList GCF_014203665.1_ASM1420366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203665.1_ASM1420366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:31,482] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:31,490] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:31,490] [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_014203665.1	s__Actinosynnema tamanrassetense	100.0	2665	2667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016907655.1	s__Actinosynnema algeriensis	87.0961	1742	2667	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	86.9875	1804	2667	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	86.4951	2029	2667	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	84.1875	1622	2667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	84.115	1641	2667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_006716745.1	s__Actinosynnema saharense	84.0488	1676	2667	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	83.9639	1678	2667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_001984175.1	s__Actinosynnema sp001984175	83.9524	1602	2667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	83.8952	1697	2667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	83.2769	1728	2667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:31,492] [INFO] GTDB search result was written to GCF_014203665.1_ASM1420366v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:31,492] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:31,495] [INFO] DFAST_QC result json was written to GCF_014203665.1_ASM1420366v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:31,496] [INFO] DFAST_QC completed!
[2024-01-25 17:50:31,496] [INFO] Total running time: 0h3m41s