[2024-01-24 13:55:57,920] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:57,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:57,922] [INFO] DQC Reference Directory: /var/lib/cwl/stgda5a3b5f-9480-4a58-9490-725319ae4e56/dqc_reference
[2024-01-24 13:55:59,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,152] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c38bf70-67b0-45b6-b638-c8feeed3d9c8/GCF_000463665.1_PG_DSM_assembly2012_genomic.fna.gz | prodigal -d GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/cds.fna -a GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:05,330] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:05,331] [INFO] Task started: HMMsearch
[2024-01-24 13:56:05,331] [INFO] Running command: hmmsearch --tblout GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda5a3b5f-9480-4a58-9490-725319ae4e56/dqc_reference/reference_markers.hmm GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:05,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:05,573] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7c38bf70-67b0-45b6-b638-c8feeed3d9c8/GCF_000463665.1_PG_DSM_assembly2012_genomic.fna.gz]
[2024-01-24 13:56:05,597] [INFO] Query marker FASTA was written to GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/markers.fasta
[2024-01-24 13:56:05,598] [INFO] Task started: Blastn
[2024-01-24 13:56:05,598] [INFO] Running command: blastn -query GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/markers.fasta -db /var/lib/cwl/stgda5a3b5f-9480-4a58-9490-725319ae4e56/dqc_reference/reference_markers.fasta -out GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:06,614] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:06,618] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:06,618] [INFO] Target genome list was writen to GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/target_genomes.txt
[2024-01-24 13:56:06,715] [INFO] Task started: fastANI
[2024-01-24 13:56:06,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c38bf70-67b0-45b6-b638-c8feeed3d9c8/GCF_000463665.1_PG_DSM_assembly2012_genomic.fna.gz --refList GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/target_genomes.txt --output GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:16,922] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:16,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda5a3b5f-9480-4a58-9490-725319ae4e56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:16,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda5a3b5f-9480-4a58-9490-725319ae4e56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:16,938] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:56:16,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:16,938] [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
Cutibacterium granulosum	strain=DSM 20700	GCA_000463665.1	33011	33011	type	True	100.0	541	549	95	conclusive
Cutibacterium granulosum	strain=DSM 20700	GCA_001700755.2	33011	33011	type	True	98.8273	528	549	95	conclusive
Cutibacterium granulosum	strain=NCTC11865	GCA_900186975.1	33011	33011	type	True	98.8117	541	549	95	conclusive
Cutibacterium avidum	strain=ATCC 25577	GCA_000227295.1	33010	33010	type	True	80.3343	238	549	95	below_threshold
Acidipropionibacterium jensenii	strain=DSM 20535	GCA_000425285.1	1749	1749	type	True	79.392	194	549	95	below_threshold
Acidipropionibacterium thoenii	strain=DSM 20276	GCA_000423445.1	1751	1751	type	True	79.2096	200	549	95	below_threshold
Acidipropionibacterium acidipropionici	strain=CGMCC 1.2230	GCA_001441165.1	1748	1748	type	True	79.0919	234	549	95	below_threshold
Acidipropionibacterium virtanenii	strain=JS278	GCA_003325455.1	2057246	2057246	type	True	78.9664	231	549	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_003030305.1	1747	1747	type	True	78.4654	145	549	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.1909	96	549	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.1761	111	549	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	76.8373	60	549	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	76.7068	75	549	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	76.3458	64	549	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	76.1474	65	549	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	76.1272	78	549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:16,940] [INFO] DFAST Taxonomy check result was written to GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/tc_result.tsv
[2024-01-24 13:56:16,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:16,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:16,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda5a3b5f-9480-4a58-9490-725319ae4e56/dqc_reference/checkm_data
[2024-01-24 13:56:16,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:16,965] [INFO] Task started: CheckM
[2024-01-24 13:56:16,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/checkm_input GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/checkm_result
[2024-01-24 13:56:56,061] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:56,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:56,083] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:56,083] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:56,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/markers.fasta)
[2024-01-24 13:56:56,084] [INFO] Task started: Blastn
[2024-01-24 13:56:56,084] [INFO] Running command: blastn -query GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/markers.fasta -db /var/lib/cwl/stgda5a3b5f-9480-4a58-9490-725319ae4e56/dqc_reference/reference_markers_gtdb.fasta -out GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:57,626] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:57,630] [INFO] Selected 9 target genomes.
[2024-01-24 13:56:57,630] [INFO] Target genome list was writen to GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:57,641] [INFO] Task started: fastANI
[2024-01-24 13:56:57,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c38bf70-67b0-45b6-b638-c8feeed3d9c8/GCF_000463665.1_PG_DSM_assembly2012_genomic.fna.gz --refList GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/target_genomes_gtdb.txt --output GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:02,113] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:02,124] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:02,124] [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_900186975.1	s__Cutibacterium granulosum	98.8117	541	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	98.45	97.35	0.97	0.94	5	conclusive
GCF_000227295.1	s__Cutibacterium avidum	80.2861	240	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	97.99	95.78	0.94	0.87	29	-
GCF_900605005.1	s__Cutibacterium timonense	80.1071	308	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425285.1	s__Acidipropionibacterium jensenii	79.392	194	549	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	79.1716	200	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	79.1117	233	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
GCF_003325455.1	s__Acidipropionibacterium virtanenii	78.9472	232	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030305.1	s__Cutibacterium acnes	78.4654	145	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.06	96.60	0.98	0.92	326	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.1641	97	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:02,126] [INFO] GTDB search result was written to GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:02,126] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:02,130] [INFO] DFAST_QC result json was written to GCF_000463665.1_PG_DSM_assembly2012_genomic.fna/dqc_result.json
[2024-01-24 13:57:02,130] [INFO] DFAST_QC completed!
[2024-01-24 13:57:02,130] [INFO] Total running time: 0h1m4s