[2024-01-24 13:49:29,393] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:29,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:29,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg91b8b1f3-8263-4c0c-bce4-23e6dea74c0f/dqc_reference
[2024-01-24 13:49:30,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:30,633] [INFO] Task started: Prodigal
[2024-01-24 13:49:30,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2d55f28-3476-41b4-af3c-389cf0969e74/GCF_014203755.1_ASM1420375v1_genomic.fna.gz | prodigal -d GCF_014203755.1_ASM1420375v1_genomic.fna/cds.fna -a GCF_014203755.1_ASM1420375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:04,586] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:04,587] [INFO] Task started: HMMsearch
[2024-01-24 13:50:04,587] [INFO] Running command: hmmsearch --tblout GCF_014203755.1_ASM1420375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91b8b1f3-8263-4c0c-bce4-23e6dea74c0f/dqc_reference/reference_markers.hmm GCF_014203755.1_ASM1420375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:05,008] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:05,009] [INFO] Found 6/6 markers.
[2024-01-24 13:50:05,078] [INFO] Query marker FASTA was written to GCF_014203755.1_ASM1420375v1_genomic.fna/markers.fasta
[2024-01-24 13:50:05,078] [INFO] Task started: Blastn
[2024-01-24 13:50:05,079] [INFO] Running command: blastn -query GCF_014203755.1_ASM1420375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91b8b1f3-8263-4c0c-bce4-23e6dea74c0f/dqc_reference/reference_markers.fasta -out GCF_014203755.1_ASM1420375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:06,438] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:06,442] [INFO] Selected 18 target genomes.
[2024-01-24 13:50:06,443] [INFO] Target genome list was writen to GCF_014203755.1_ASM1420375v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:06,450] [INFO] Task started: fastANI
[2024-01-24 13:50:06,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d55f28-3476-41b4-af3c-389cf0969e74/GCF_014203755.1_ASM1420375v1_genomic.fna.gz --refList GCF_014203755.1_ASM1420375v1_genomic.fna/target_genomes.txt --output GCF_014203755.1_ASM1420375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:45,864] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:45,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91b8b1f3-8263-4c0c-bce4-23e6dea74c0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:45,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91b8b1f3-8263-4c0c-bce4-23e6dea74c0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:45,880] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:45,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:45,881] [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 violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	100.0	2451	2451	95	conclusive
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	82.4217	1346	2451	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	82.3524	1498	2451	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	82.3137	1408	2451	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	82.3129	1381	2451	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	82.2681	1374	2451	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	82.1916	1383	2451	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	82.1588	1402	2451	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	82.1563	1433	2451	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	82.1301	1400	2451	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	82.0383	1369	2451	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	81.9738	1260	2451	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	81.8361	1482	2451	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	81.7155	1496	2451	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.8858	933	2451	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.7085	895	2451	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.1907	786	2451	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.8806	976	2451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,885] [INFO] DFAST Taxonomy check result was written to GCF_014203755.1_ASM1420375v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:45,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:45,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:45,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91b8b1f3-8263-4c0c-bce4-23e6dea74c0f/dqc_reference/checkm_data
[2024-01-24 13:50:45,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:45,962] [INFO] Task started: CheckM
[2024-01-24 13:50:45,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203755.1_ASM1420375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203755.1_ASM1420375v1_genomic.fna/checkm_input GCF_014203755.1_ASM1420375v1_genomic.fna/checkm_result
[2024-01-24 13:53:18,847] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:18,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:18,878] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:18,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:18,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203755.1_ASM1420375v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:18,879] [INFO] Task started: Blastn
[2024-01-24 13:53:18,879] [INFO] Running command: blastn -query GCF_014203755.1_ASM1420375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91b8b1f3-8263-4c0c-bce4-23e6dea74c0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203755.1_ASM1420375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:20,953] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:20,962] [INFO] Selected 16 target genomes.
[2024-01-24 13:53:20,962] [INFO] Target genome list was writen to GCF_014203755.1_ASM1420375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:21,009] [INFO] Task started: fastANI
[2024-01-24 13:53:21,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d55f28-3476-41b4-af3c-389cf0969e74/GCF_014203755.1_ASM1420375v1_genomic.fna.gz --refList GCF_014203755.1_ASM1420375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203755.1_ASM1420375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:54,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:54,271] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:54,272] [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_014203755.1	s__Actinosynnema violaceirubrum	100.0	2449	2451	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	82.434	1347	2451	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	82.3447	1501	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716745.1	s__Actinosynnema saharense	82.3153	1408	2451	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	82.2819	1388	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	82.2392	1380	2451	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	82.1873	1393	2451	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	82.1846	1438	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_001280085.1	s__Actinosynnema sp001280085	82.1793	1422	2451	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	82.167	1386	2451	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	82.1515	1406	2451	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	82.0297	1315	2451	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	81.8276	1480	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014648515.1	s__Actinosynnema coeruleofuscum	81.8273	1255	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_002354875.1	s__Actinosynnema auranticum	80.9783	1253	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	100.00	100.00	1.00	1.00	2	-
GCF_014203355.1	s__Kutzneria kofuensis	78.7296	954	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:54,273] [INFO] GTDB search result was written to GCF_014203755.1_ASM1420375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:54,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:54,277] [INFO] DFAST_QC result json was written to GCF_014203755.1_ASM1420375v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:54,277] [INFO] DFAST_QC completed!
[2024-01-24 13:53:54,277] [INFO] Total running time: 0h4m25s