[2024-01-24 10:47:11,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg63c8c8b2-00ec-4c3d-902d-350fed2b6b77/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg52d08b98-d874-4864-bf3d-1f566d6b89f7/GCF_016907655.1_ASM1690765v1_genomic.fna.gz | prodigal -d GCF_016907655.1_ASM1690765v1_genomic.fna/cds.fna -a GCF_016907655.1_ASM1690765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:39,450] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:39,450] [INFO] Task started: HMMsearch
[2024-01-24 10:47:39,451] [INFO] Running command: hmmsearch --tblout GCF_016907655.1_ASM1690765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63c8c8b2-00ec-4c3d-902d-350fed2b6b77/dqc_reference/reference_markers.hmm GCF_016907655.1_ASM1690765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:39,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:39,800] [INFO] Found 6/6 markers.
[2024-01-24 10:47:39,941] [INFO] Query marker FASTA was written to GCF_016907655.1_ASM1690765v1_genomic.fna/markers.fasta
[2024-01-24 10:47:39,941] [INFO] Task started: Blastn
[2024-01-24 10:47:39,941] [INFO] Running command: blastn -query GCF_016907655.1_ASM1690765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63c8c8b2-00ec-4c3d-902d-350fed2b6b77/dqc_reference/reference_markers.fasta -out GCF_016907655.1_ASM1690765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:41,314] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:41,319] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:41,319] [INFO] Target genome list was writen to GCF_016907655.1_ASM1690765v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:41,340] [INFO] Task started: fastANI
[2024-01-24 10:47:41,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg52d08b98-d874-4864-bf3d-1f566d6b89f7/GCF_016907655.1_ASM1690765v1_genomic.fna.gz --refList GCF_016907655.1_ASM1690765v1_genomic.fna/target_genomes.txt --output GCF_016907655.1_ASM1690765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:17,135] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:17,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63c8c8b2-00ec-4c3d-902d-350fed2b6b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:17,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63c8c8b2-00ec-4c3d-902d-350fed2b6b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:17,149] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:17,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:17,149] [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 algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	100.0	2292	2292	95	conclusive
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	87.7183	1689	2292	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	87.3781	1718	2292	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	85.7381	1738	2292	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	85.0966	1614	2292	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	84.6797	1547	2292	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	84.0438	1538	2292	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	83.9254	1606	2292	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	83.8757	1503	2292	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	83.8558	1591	2292	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	83.1719	1435	2292	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	79.1649	988	2292	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	79.131	929	2292	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.6294	932	2292	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.1293	807	2292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:17,152] [INFO] DFAST Taxonomy check result was written to GCF_016907655.1_ASM1690765v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:17,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:17,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:17,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63c8c8b2-00ec-4c3d-902d-350fed2b6b77/dqc_reference/checkm_data
[2024-01-24 10:48:17,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:17,221] [INFO] Task started: CheckM
[2024-01-24 10:48:17,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907655.1_ASM1690765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907655.1_ASM1690765v1_genomic.fna/checkm_input GCF_016907655.1_ASM1690765v1_genomic.fna/checkm_result
[2024-01-24 10:50:24,355] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:24,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:24,385] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:24,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:24,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907655.1_ASM1690765v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:24,386] [INFO] Task started: Blastn
[2024-01-24 10:50:24,387] [INFO] Running command: blastn -query GCF_016907655.1_ASM1690765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63c8c8b2-00ec-4c3d-902d-350fed2b6b77/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907655.1_ASM1690765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:26,490] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:26,494] [INFO] Selected 12 target genomes.
[2024-01-24 10:50:26,495] [INFO] Target genome list was writen to GCF_016907655.1_ASM1690765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:26,505] [INFO] Task started: fastANI
[2024-01-24 10:50:26,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg52d08b98-d874-4864-bf3d-1f566d6b89f7/GCF_016907655.1_ASM1690765v1_genomic.fna.gz --refList GCF_016907655.1_ASM1690765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907655.1_ASM1690765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:56,333] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:56,354] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:56,355] [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_016907655.1	s__Actinosynnema algeriensis	100.0	2292	2292	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_003634935.1	s__Actinosynnema australiense	87.595	1705	2292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	87.37	1719	2292	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	85.6872	1746	2292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	84.6737	1547	2292	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	84.0765	1534	2292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_003014735.1	s__Actinosynnema carneum	83.8542	1507	2292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_009498035.1	s__Actinosynnema syringae	83.825	1626	2292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001984175.1	s__Actinosynnema sp001984175	83.5894	1429	2292	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	83.4348	1450	2292	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	83.2385	1425	2292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	82.4349	1335	2292	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 10:50:56,357] [INFO] GTDB search result was written to GCF_016907655.1_ASM1690765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:56,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:56,364] [INFO] DFAST_QC result json was written to GCF_016907655.1_ASM1690765v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:56,364] [INFO] DFAST_QC completed!
[2024-01-24 10:50:56,365] [INFO] Total running time: 0h3m45s