[2024-01-24 11:48:21,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,281] [INFO] DQC Reference Directory: /var/lib/cwl/stga0269400-7ea8-4bae-b689-5fc2ca71edb7/dqc_reference
[2024-01-24 11:48:24,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,563] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,563] [INFO] Running command: gunzip -c /var/lib/cwl/stgd55f7fa9-370b-4e28-9f93-27f4fce34a7c/GCF_016907695.1_ASM1690769v1_genomic.fna.gz | prodigal -d GCF_016907695.1_ASM1690769v1_genomic.fna/cds.fna -a GCF_016907695.1_ASM1690769v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:54,188] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:54,189] [INFO] Task started: HMMsearch
[2024-01-24 11:48:54,189] [INFO] Running command: hmmsearch --tblout GCF_016907695.1_ASM1690769v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0269400-7ea8-4bae-b689-5fc2ca71edb7/dqc_reference/reference_markers.hmm GCF_016907695.1_ASM1690769v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:54,540] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:54,541] [INFO] Found 6/6 markers.
[2024-01-24 11:48:54,600] [INFO] Query marker FASTA was written to GCF_016907695.1_ASM1690769v1_genomic.fna/markers.fasta
[2024-01-24 11:48:54,600] [INFO] Task started: Blastn
[2024-01-24 11:48:54,600] [INFO] Running command: blastn -query GCF_016907695.1_ASM1690769v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0269400-7ea8-4bae-b689-5fc2ca71edb7/dqc_reference/reference_markers.fasta -out GCF_016907695.1_ASM1690769v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:55,942] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:55,945] [INFO] Selected 10 target genomes.
[2024-01-24 11:48:55,946] [INFO] Target genome list was writen to GCF_016907695.1_ASM1690769v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:55,951] [INFO] Task started: fastANI
[2024-01-24 11:48:55,951] [INFO] Running command: fastANI --query /var/lib/cwl/stgd55f7fa9-370b-4e28-9f93-27f4fce34a7c/GCF_016907695.1_ASM1690769v1_genomic.fna.gz --refList GCF_016907695.1_ASM1690769v1_genomic.fna/target_genomes.txt --output GCF_016907695.1_ASM1690769v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:49:16,873] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:16,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0269400-7ea8-4bae-b689-5fc2ca71edb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:49:16,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0269400-7ea8-4bae-b689-5fc2ca71edb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:49:16,885] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:49:16,885] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:49:16,885] [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
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	100.0	2560	2560	95	conclusive
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	90.0089	2142	2560	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	86.7263	1831	2560	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	86.7024	1881	2560	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	86.6837	1877	2560	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	83.0837	1515	2560	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	82.0632	1132	2560	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.6447	804	2560	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	78.5531	947	2560	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	76.5835	632	2560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:49:16,887] [INFO] DFAST Taxonomy check result was written to GCF_016907695.1_ASM1690769v1_genomic.fna/tc_result.tsv
[2024-01-24 11:49:16,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:49:16,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:49:16,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0269400-7ea8-4bae-b689-5fc2ca71edb7/dqc_reference/checkm_data
[2024-01-24 11:49:16,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:49:16,960] [INFO] Task started: CheckM
[2024-01-24 11:49:16,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907695.1_ASM1690769v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907695.1_ASM1690769v1_genomic.fna/checkm_input GCF_016907695.1_ASM1690769v1_genomic.fna/checkm_result
[2024-01-24 11:51:05,654] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:05,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:05,678] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:05,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:05,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907695.1_ASM1690769v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:05,679] [INFO] Task started: Blastn
[2024-01-24 11:51:05,679] [INFO] Running command: blastn -query GCF_016907695.1_ASM1690769v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0269400-7ea8-4bae-b689-5fc2ca71edb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907695.1_ASM1690769v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:07,757] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:07,761] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:07,761] [INFO] Target genome list was writen to GCF_016907695.1_ASM1690769v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:07,771] [INFO] Task started: fastANI
[2024-01-24 11:51:07,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgd55f7fa9-370b-4e28-9f93-27f4fce34a7c/GCF_016907695.1_ASM1690769v1_genomic.fna.gz --refList GCF_016907695.1_ASM1690769v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907695.1_ASM1690769v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:30,872] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:30,887] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:30,887] [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_016907695.1	s__Actinokineospora baliensis	100.0	2560	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111175.1	s__Actinokineospora terrae	86.6812	1877	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_000482865.1	s__Actinokineospora inagensis	84.1592	1566	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	83.1084	1512	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	82.9351	1420	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	82.0871	1131	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182415.1	s__Actinokineospora mzabensis	81.5869	1224	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_001940455.1	s__Actinokineospora bangkokensis	81.3751	1196	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323725.1	s__Actinokineospora xionganensis	81.0031	1046	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354875.1	s__Actinosynnema auranticum	78.7908	986	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	100.00	100.00	1.00	1.00	2	-
GCA_009379765.1	s__Actinophytocola sp009379765	78.7817	838	2560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:30,890] [INFO] GTDB search result was written to GCF_016907695.1_ASM1690769v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:30,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:30,895] [INFO] DFAST_QC result json was written to GCF_016907695.1_ASM1690769v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:30,895] [INFO] DFAST_QC completed!
[2024-01-24 11:51:30,895] [INFO] Total running time: 0h3m10s