[2024-01-25 19:45:50,553] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:50,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:50,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgeebc1feb-5d58-4ce2-a304-24ff285b9149/dqc_reference
[2024-01-25 19:45:51,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:51,696] [INFO] Task started: Prodigal
[2024-01-25 19:45:51,696] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1f4e1f7-4ba1-44b6-981b-2322658ca700/GCF_000374445.1_ASM37444v1_genomic.fna.gz | prodigal -d GCF_000374445.1_ASM37444v1_genomic.fna/cds.fna -a GCF_000374445.1_ASM37444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:16,763] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:16,764] [INFO] Task started: HMMsearch
[2024-01-25 19:46:16,764] [INFO] Running command: hmmsearch --tblout GCF_000374445.1_ASM37444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeebc1feb-5d58-4ce2-a304-24ff285b9149/dqc_reference/reference_markers.hmm GCF_000374445.1_ASM37444v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:17,086] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:17,087] [INFO] Found 6/6 markers.
[2024-01-25 19:46:17,147] [INFO] Query marker FASTA was written to GCF_000374445.1_ASM37444v1_genomic.fna/markers.fasta
[2024-01-25 19:46:17,147] [INFO] Task started: Blastn
[2024-01-25 19:46:17,147] [INFO] Running command: blastn -query GCF_000374445.1_ASM37444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeebc1feb-5d58-4ce2-a304-24ff285b9149/dqc_reference/reference_markers.fasta -out GCF_000374445.1_ASM37444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:18,379] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:18,384] [INFO] Selected 15 target genomes.
[2024-01-25 19:46:18,384] [INFO] Target genome list was writen to GCF_000374445.1_ASM37444v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:18,396] [INFO] Task started: fastANI
[2024-01-25 19:46:18,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1f4e1f7-4ba1-44b6-981b-2322658ca700/GCF_000374445.1_ASM37444v1_genomic.fna.gz --refList GCF_000374445.1_ASM37444v1_genomic.fna/target_genomes.txt --output GCF_000374445.1_ASM37444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:46,950] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:46,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeebc1feb-5d58-4ce2-a304-24ff285b9149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:46,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeebc1feb-5d58-4ce2-a304-24ff285b9149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:46,965] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:46,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:46,965] [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 enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	100.0	2658	2662	95	conclusive
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	83.596	1609	2662	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	83.2544	1360	2662	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	83.0731	1445	2662	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	82.9861	1437	2662	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	82.9147	1431	2662	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	82.9007	1424	2662	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	82.0	1108	2662	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	81.1882	1181	2662	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	80.8467	1124	2662	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	80.836	1195	2662	95	below_threshold
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	80.6675	1065	2662	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.5255	846	2662	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.1223	831	2662	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.8921	1009	2662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:46,966] [INFO] DFAST Taxonomy check result was written to GCF_000374445.1_ASM37444v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:46,967] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:46,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:46,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeebc1feb-5d58-4ce2-a304-24ff285b9149/dqc_reference/checkm_data
[2024-01-25 19:46:46,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:47,040] [INFO] Task started: CheckM
[2024-01-25 19:46:47,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374445.1_ASM37444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374445.1_ASM37444v1_genomic.fna/checkm_input GCF_000374445.1_ASM37444v1_genomic.fna/checkm_result
[2024-01-25 19:48:25,389] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:25,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:25,439] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:25,440] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:25,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374445.1_ASM37444v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:25,441] [INFO] Task started: Blastn
[2024-01-25 19:48:25,441] [INFO] Running command: blastn -query GCF_000374445.1_ASM37444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeebc1feb-5d58-4ce2-a304-24ff285b9149/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374445.1_ASM37444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:27,415] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:27,418] [INFO] Selected 11 target genomes.
[2024-01-25 19:48:27,418] [INFO] Target genome list was writen to GCF_000374445.1_ASM37444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:27,429] [INFO] Task started: fastANI
[2024-01-25 19:48:27,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1f4e1f7-4ba1-44b6-981b-2322658ca700/GCF_000374445.1_ASM37444v1_genomic.fna.gz --refList GCF_000374445.1_ASM37444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374445.1_ASM37444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:50,403] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:50,411] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:50,411] [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_000374445.1	s__Actinokineospora enzanensis	100.0	2657	2662	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_002934265.1	s__Actinokineospora auranticolor	83.6088	1609	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482865.1	s__Actinokineospora inagensis	83.2086	1366	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	83.0493	1448	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_016907695.1	s__Actinokineospora baliensis	82.8935	1427	2662	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	82.0004	1108	2662	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	81.2513	1211	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_900070365.1	s__Actinokineospora sp900070365	80.9097	1061	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	80.8428	1125	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940455.1	s__Actinokineospora bangkokensis	80.8426	1194	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362515.1	s__Actinokineospora alba	80.6382	1071	2662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:50,413] [INFO] GTDB search result was written to GCF_000374445.1_ASM37444v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:50,413] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:50,418] [INFO] DFAST_QC result json was written to GCF_000374445.1_ASM37444v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:50,418] [INFO] DFAST_QC completed!
[2024-01-25 19:48:50,418] [INFO] Total running time: 0h2m60s