[2024-01-24 12:44:43,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,763] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcd36cc3-b1f6-4f93-9b04-3ee78b3d3c81/dqc_reference
[2024-01-24 12:44:45,199] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,199] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg947eddf5-fb29-42cf-9c1c-2c0103534aa6/GCF_028622115.1_ASM2862211v1_genomic.fna.gz | prodigal -d GCF_028622115.1_ASM2862211v1_genomic.fna/cds.fna -a GCF_028622115.1_ASM2862211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:24,181] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:24,182] [INFO] Task started: HMMsearch
[2024-01-24 12:45:24,182] [INFO] Running command: hmmsearch --tblout GCF_028622115.1_ASM2862211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcd36cc3-b1f6-4f93-9b04-3ee78b3d3c81/dqc_reference/reference_markers.hmm GCF_028622115.1_ASM2862211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:24,642] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:24,644] [INFO] Found 6/6 markers.
[2024-01-24 12:45:24,727] [INFO] Query marker FASTA was written to GCF_028622115.1_ASM2862211v1_genomic.fna/markers.fasta
[2024-01-24 12:45:24,727] [INFO] Task started: Blastn
[2024-01-24 12:45:24,727] [INFO] Running command: blastn -query GCF_028622115.1_ASM2862211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcd36cc3-b1f6-4f93-9b04-3ee78b3d3c81/dqc_reference/reference_markers.fasta -out GCF_028622115.1_ASM2862211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:26,190] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:26,195] [INFO] Selected 23 target genomes.
[2024-01-24 12:45:26,195] [INFO] Target genome list was writen to GCF_028622115.1_ASM2862211v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:26,226] [INFO] Task started: fastANI
[2024-01-24 12:45:26,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg947eddf5-fb29-42cf-9c1c-2c0103534aa6/GCF_028622115.1_ASM2862211v1_genomic.fna.gz --refList GCF_028622115.1_ASM2862211v1_genomic.fna/target_genomes.txt --output GCF_028622115.1_ASM2862211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:09,264] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:09,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcd36cc3-b1f6-4f93-9b04-3ee78b3d3c81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:09,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcd36cc3-b1f6-4f93-9b04-3ee78b3d3c81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:09,288] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:46:09,288] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:46:09,288] [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
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	88.5602	2532	3470	95	below_threshold
Kutzneria buriramensis	strain=DSM 45791	GCA_003387475.1	1045776	1045776	type	True	86.9442	2507	3470	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	79.195	1119	3470	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	79.0352	1115	3470	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	78.7761	1179	3470	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.6516	937	3470	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	78.6414	1134	3470	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	78.6378	1249	3470	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	78.573	926	3470	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	78.5454	1375	3470	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	78.5219	1359	3470	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	78.4891	975	3470	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	78.4854	852	3470	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	78.4831	1064	3470	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.4759	897	3470	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	78.4751	1038	3470	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	78.4558	931	3470	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	78.3868	1027	3470	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.3707	892	3470	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	78.2121	1091	3470	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	78.0662	1259	3470	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	78.0306	1191	3470	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.6897	839	3470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:09,291] [INFO] DFAST Taxonomy check result was written to GCF_028622115.1_ASM2862211v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:09,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:09,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:09,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcd36cc3-b1f6-4f93-9b04-3ee78b3d3c81/dqc_reference/checkm_data
[2024-01-24 12:46:09,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:09,391] [INFO] Task started: CheckM
[2024-01-24 12:46:09,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028622115.1_ASM2862211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028622115.1_ASM2862211v1_genomic.fna/checkm_input GCF_028622115.1_ASM2862211v1_genomic.fna/checkm_result
[2024-01-24 12:48:57,751] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:57,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:57,781] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:57,782] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:57,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028622115.1_ASM2862211v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:57,782] [INFO] Task started: Blastn
[2024-01-24 12:48:57,783] [INFO] Running command: blastn -query GCF_028622115.1_ASM2862211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcd36cc3-b1f6-4f93-9b04-3ee78b3d3c81/dqc_reference/reference_markers_gtdb.fasta -out GCF_028622115.1_ASM2862211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:59,858] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:59,863] [INFO] Selected 11 target genomes.
[2024-01-24 12:48:59,864] [INFO] Target genome list was writen to GCF_028622115.1_ASM2862211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:59,871] [INFO] Task started: fastANI
[2024-01-24 12:48:59,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg947eddf5-fb29-42cf-9c1c-2c0103534aa6/GCF_028622115.1_ASM2862211v1_genomic.fna.gz --refList GCF_028622115.1_ASM2862211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028622115.1_ASM2862211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:29,259] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:29,272] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:49:29,272] [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_000568255.1	s__Kutzneria sp000568255	89.0267	2654	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203355.1	s__Kutzneria kofuensis	88.5911	2526	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263855.1	s__Kutzneria sp018263855	87.3643	2515	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387475.1	s__Kutzneria buriramensis	86.9457	2507	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138725.1	s__Kutzneria viridogrisea	80.9622	1577	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	99.33	99.33	0.95	0.95	2	-
GCF_006716745.1	s__Actinosynnema saharense	78.7198	1188	3470	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	78.6536	1107	3470	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	78.645	1248	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_009769385.1	s__Actinosynnema deserti	78.5853	1151	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023245.1	s__Actinosynnema mirum	78.4315	1073	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	99.51	99.51	0.95	0.95	3	-
GCF_003182415.1	s__Actinokineospora mzabensis	78.4291	994	3470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:29,274] [INFO] GTDB search result was written to GCF_028622115.1_ASM2862211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:29,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:29,278] [INFO] DFAST_QC result json was written to GCF_028622115.1_ASM2862211v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:29,278] [INFO] DFAST_QC completed!
[2024-01-24 12:49:29,278] [INFO] Total running time: 0h4m46s