[2024-01-24 13:46:18,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,493] [INFO] DQC Reference Directory: /var/lib/cwl/stgd997e740-8219-4e37-825e-8836d8913094/dqc_reference
[2024-01-24 13:46:19,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,862] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,862] [INFO] Running command: gunzip -c /var/lib/cwl/stgeca24b25-a43a-4f2f-9b1c-4ed6f72b183e/GCF_000427845.1_ASM42784v1_genomic.fna.gz | prodigal -d GCF_000427845.1_ASM42784v1_genomic.fna/cds.fna -a GCF_000427845.1_ASM42784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:30,871] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:30,871] [INFO] Task started: HMMsearch
[2024-01-24 13:46:30,871] [INFO] Running command: hmmsearch --tblout GCF_000427845.1_ASM42784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd997e740-8219-4e37-825e-8836d8913094/dqc_reference/reference_markers.hmm GCF_000427845.1_ASM42784v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:31,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:31,205] [INFO] Found 6/6 markers.
[2024-01-24 13:46:31,250] [INFO] Query marker FASTA was written to GCF_000427845.1_ASM42784v1_genomic.fna/markers.fasta
[2024-01-24 13:46:31,250] [INFO] Task started: Blastn
[2024-01-24 13:46:31,250] [INFO] Running command: blastn -query GCF_000427845.1_ASM42784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd997e740-8219-4e37-825e-8836d8913094/dqc_reference/reference_markers.fasta -out GCF_000427845.1_ASM42784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:32,418] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:32,421] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:32,421] [INFO] Target genome list was writen to GCF_000427845.1_ASM42784v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:32,429] [INFO] Task started: fastANI
[2024-01-24 13:46:32,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgeca24b25-a43a-4f2f-9b1c-4ed6f72b183e/GCF_000427845.1_ASM42784v1_genomic.fna.gz --refList GCF_000427845.1_ASM42784v1_genomic.fna/target_genomes.txt --output GCF_000427845.1_ASM42784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:42,400] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:42,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd997e740-8219-4e37-825e-8836d8913094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:42,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd997e740-8219-4e37-825e-8836d8913094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:42,411] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:42,411] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:42,411] [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	100.0	1171	1172	95	conclusive
Acidipropionibacterium acidipropionici	strain=CGMCC 1.2230	GCA_001441165.1	1748	1748	type	True	99.9929	1171	1172	95	conclusive
Acidipropionibacterium virtanenii	strain=JS278	GCA_003325455.1	2057246	2057246	type	True	87.2531	892	1172	95	below_threshold
Acidipropionibacterium jensenii	strain=DSM 20535	GCA_000425285.1	1749	1749	type	True	82.8534	664	1172	95	below_threshold
Acidipropionibacterium thoenii	strain=DSM 20276	GCA_000423445.1	1751	1751	type	True	82.1544	610	1172	95	below_threshold
Brooklawnia cerclae	strain=DSM 19609	GCA_011758645.1	349934	349934	type	True	77.6242	190	1172	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	76.8913	188	1172	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.7728	191	1172	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	76.3068	188	1172	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	76.2184	229	1172	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	76.1958	193	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:42,412] [INFO] DFAST Taxonomy check result was written to GCF_000427845.1_ASM42784v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:42,413] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:42,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:42,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd997e740-8219-4e37-825e-8836d8913094/dqc_reference/checkm_data
[2024-01-24 13:46:42,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:42,449] [INFO] Task started: CheckM
[2024-01-24 13:46:42,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000427845.1_ASM42784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000427845.1_ASM42784v1_genomic.fna/checkm_input GCF_000427845.1_ASM42784v1_genomic.fna/checkm_result
[2024-01-24 13:47:35,776] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:35,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:35,799] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:35,799] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:35,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000427845.1_ASM42784v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:35,801] [INFO] Task started: Blastn
[2024-01-24 13:47:35,801] [INFO] Running command: blastn -query GCF_000427845.1_ASM42784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd997e740-8219-4e37-825e-8836d8913094/dqc_reference/reference_markers_gtdb.fasta -out GCF_000427845.1_ASM42784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:37,568] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:37,572] [INFO] Selected 8 target genomes.
[2024-01-24 13:47:37,572] [INFO] Target genome list was writen to GCF_000427845.1_ASM42784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:37,582] [INFO] Task started: fastANI
[2024-01-24 13:47:37,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgeca24b25-a43a-4f2f-9b1c-4ed6f72b183e/GCF_000427845.1_ASM42784v1_genomic.fna.gz --refList GCF_000427845.1_ASM42784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000427845.1_ASM42784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:43,672] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:43,680] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:43,681] [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_001441165.1	s__Acidipropionibacterium acidipropionici	99.9929	1171	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	conclusive
GCF_003325455.1	s__Acidipropionibacterium virtanenii	87.257	892	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425285.1	s__Acidipropionibacterium jensenii	82.8596	664	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	98.58	97.66	0.92	0.89	5	-
GCF_000423445.1	s__Acidipropionibacterium thoenii	82.1561	610	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900605005.1	s__Cutibacterium timonense	80.4495	481	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758645.1	s__Brooklawnia cerclae	77.6092	190	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brooklawnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.5032	271	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_014137855.1	s__Friedmanniella_A endophytica	77.2725	244	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:43,682] [INFO] GTDB search result was written to GCF_000427845.1_ASM42784v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:43,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:43,687] [INFO] DFAST_QC result json was written to GCF_000427845.1_ASM42784v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:43,687] [INFO] DFAST_QC completed!
[2024-01-24 13:47:43,688] [INFO] Total running time: 0h1m25s