[2024-01-24 12:15:20,829] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,833] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb97eb36-c54e-4f24-8d55-83f1379d4474/dqc_reference
[2024-01-24 12:15:22,122] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,123] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,123] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b73fe72-6bb3-45a6-bff5-b7b00e24ca6e/GCF_900605005.1_PRJEB25873_genomic.fna.gz | prodigal -d GCF_900605005.1_PRJEB25873_genomic.fna/cds.fna -a GCF_900605005.1_PRJEB25873_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:30,699] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:30,700] [INFO] Task started: HMMsearch
[2024-01-24 12:15:30,700] [INFO] Running command: hmmsearch --tblout GCF_900605005.1_PRJEB25873_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb97eb36-c54e-4f24-8d55-83f1379d4474/dqc_reference/reference_markers.hmm GCF_900605005.1_PRJEB25873_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:30,955] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:30,956] [INFO] Found 6/6 markers.
[2024-01-24 12:15:30,986] [INFO] Query marker FASTA was written to GCF_900605005.1_PRJEB25873_genomic.fna/markers.fasta
[2024-01-24 12:15:30,987] [INFO] Task started: Blastn
[2024-01-24 12:15:30,987] [INFO] Running command: blastn -query GCF_900605005.1_PRJEB25873_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb97eb36-c54e-4f24-8d55-83f1379d4474/dqc_reference/reference_markers.fasta -out GCF_900605005.1_PRJEB25873_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:32,052] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:32,058] [INFO] Selected 18 target genomes.
[2024-01-24 12:15:32,059] [INFO] Target genome list was writen to GCF_900605005.1_PRJEB25873_genomic.fna/target_genomes.txt
[2024-01-24 12:15:32,066] [INFO] Task started: fastANI
[2024-01-24 12:15:32,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b73fe72-6bb3-45a6-bff5-b7b00e24ca6e/GCF_900605005.1_PRJEB25873_genomic.fna.gz --refList GCF_900605005.1_PRJEB25873_genomic.fna/target_genomes.txt --output GCF_900605005.1_PRJEB25873_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:42,119] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:42,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb97eb36-c54e-4f24-8d55-83f1379d4474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:42,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb97eb36-c54e-4f24-8d55-83f1379d4474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:42,137] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:42,137] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:42,137] [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
Acidipropionibacterium acidipropionici	strain=DSM 4900	GCA_000427845.1	1748	1748	type	True	80.7093	470	931	95	below_threshold
Acidipropionibacterium acidipropionici	strain=CGMCC 1.2230	GCA_001441165.1	1748	1748	type	True	80.6801	498	931	95	below_threshold
Cutibacterium granulosum	strain=NCTC11865	GCA_900186975.1	33011	33011	type	True	80.5261	390	931	95	below_threshold
Acidipropionibacterium jensenii	strain=DSM 20535	GCA_000425285.1	1749	1749	type	True	80.4956	440	931	95	below_threshold
Cutibacterium granulosum	strain=DSM 20700	GCA_001700755.2	33011	33011	type	True	80.3993	381	931	95	below_threshold
Acidipropionibacterium virtanenii	strain=JS278	GCA_003325455.1	2057246	2057246	type	True	80.389	443	931	95	below_threshold
Cutibacterium granulosum	strain=DSM 20700	GCA_000463665.1	33011	33011	type	True	80.2982	313	931	95	below_threshold
Cutibacterium avidum	strain=ATCC 25577	GCA_000227295.1	33010	33010	type	True	80.2479	397	931	95	below_threshold
Acidipropionibacterium thoenii	strain=DSM 20276	GCA_000423445.1	1751	1751	type	True	79.9851	397	931	95	below_threshold
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	77.9243	211	931	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.7891	250	931	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.6861	249	931	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	77.6219	246	931	95	below_threshold
Arachnia rubra	strain=SK-1	GCA_019973735.1	1547448	1547448	type	True	77.616	111	931	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	77.5876	216	931	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	77.1247	182	931	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	76.9602	204	931	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.7741	190	931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,139] [INFO] DFAST Taxonomy check result was written to GCF_900605005.1_PRJEB25873_genomic.fna/tc_result.tsv
[2024-01-24 12:15:42,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:42,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:42,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb97eb36-c54e-4f24-8d55-83f1379d4474/dqc_reference/checkm_data
[2024-01-24 12:15:42,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:42,173] [INFO] Task started: CheckM
[2024-01-24 12:15:42,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900605005.1_PRJEB25873_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900605005.1_PRJEB25873_genomic.fna/checkm_input GCF_900605005.1_PRJEB25873_genomic.fna/checkm_result
[2024-01-24 12:16:44,502] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:44,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:44,526] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:44,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:44,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900605005.1_PRJEB25873_genomic.fna/markers.fasta)
[2024-01-24 12:16:44,527] [INFO] Task started: Blastn
[2024-01-24 12:16:44,527] [INFO] Running command: blastn -query GCF_900605005.1_PRJEB25873_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb97eb36-c54e-4f24-8d55-83f1379d4474/dqc_reference/reference_markers_gtdb.fasta -out GCF_900605005.1_PRJEB25873_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:46,101] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:46,106] [INFO] Selected 11 target genomes.
[2024-01-24 12:16:46,106] [INFO] Target genome list was writen to GCF_900605005.1_PRJEB25873_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:46,114] [INFO] Task started: fastANI
[2024-01-24 12:16:46,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b73fe72-6bb3-45a6-bff5-b7b00e24ca6e/GCF_900605005.1_PRJEB25873_genomic.fna.gz --refList GCF_900605005.1_PRJEB25873_genomic.fna/target_genomes_gtdb.txt --output GCF_900605005.1_PRJEB25873_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:53,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:53,581] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:53,581] [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_900605005.1	s__Cutibacterium timonense	100.0	924	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	80.7648	493	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
GCF_900186975.1	s__Cutibacterium granulosum	80.5393	391	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	98.45	97.35	0.97	0.94	5	-
GCF_000425285.1	s__Acidipropionibacterium jensenii	80.509	439	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	98.58	97.66	0.92	0.89	5	-
GCF_003325455.1	s__Acidipropionibacterium virtanenii	80.3479	441	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227295.1	s__Cutibacterium avidum	80.2348	398	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	97.99	95.78	0.94	0.87	29	-
GCF_000423445.1	s__Acidipropionibacterium thoenii	79.9201	402	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569205.1	s__Brevilactibacter sp014164685	77.8197	254	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	99.00	98.00	0.92	0.83	3	-
GCF_018128325.1	s__Arachnia rubra	77.7185	111	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	99.26	99.21	0.97	0.97	4	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.6421	224	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCA_012838755.1	s__Brevilactibacter sp012838755	77.5272	218	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:53,583] [INFO] GTDB search result was written to GCF_900605005.1_PRJEB25873_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:53,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:53,589] [INFO] DFAST_QC result json was written to GCF_900605005.1_PRJEB25873_genomic.fna/dqc_result.json
[2024-01-24 12:16:53,589] [INFO] DFAST_QC completed!
[2024-01-24 12:16:53,589] [INFO] Total running time: 0h1m33s