[2024-01-24 13:28:39,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:39,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:39,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg969906c6-801c-4510-9270-b6b76f02628e/dqc_reference
[2024-01-24 13:28:41,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:41,145] [INFO] Task started: Prodigal
[2024-01-24 13:28:41,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg6485b970-8dbf-4e4f-b19f-4e43929bc63c/GCF_000423445.1_ASM42344v1_genomic.fna.gz | prodigal -d GCF_000423445.1_ASM42344v1_genomic.fna/cds.fna -a GCF_000423445.1_ASM42344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:49,712] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:49,712] [INFO] Task started: HMMsearch
[2024-01-24 13:28:49,713] [INFO] Running command: hmmsearch --tblout GCF_000423445.1_ASM42344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg969906c6-801c-4510-9270-b6b76f02628e/dqc_reference/reference_markers.hmm GCF_000423445.1_ASM42344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:49,964] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:49,966] [INFO] Found 6/6 markers.
[2024-01-24 13:28:49,997] [INFO] Query marker FASTA was written to GCF_000423445.1_ASM42344v1_genomic.fna/markers.fasta
[2024-01-24 13:28:49,997] [INFO] Task started: Blastn
[2024-01-24 13:28:49,998] [INFO] Running command: blastn -query GCF_000423445.1_ASM42344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg969906c6-801c-4510-9270-b6b76f02628e/dqc_reference/reference_markers.fasta -out GCF_000423445.1_ASM42344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:51,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:51,036] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:51,037] [INFO] Target genome list was writen to GCF_000423445.1_ASM42344v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:51,051] [INFO] Task started: fastANI
[2024-01-24 13:28:51,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg6485b970-8dbf-4e4f-b19f-4e43929bc63c/GCF_000423445.1_ASM42344v1_genomic.fna.gz --refList GCF_000423445.1_ASM42344v1_genomic.fna/target_genomes.txt --output GCF_000423445.1_ASM42344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:01,538] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:01,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg969906c6-801c-4510-9270-b6b76f02628e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:01,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg969906c6-801c-4510-9270-b6b76f02628e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:01,551] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:01,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:01,551] [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 thoenii	strain=DSM 20276	GCA_000423445.1	1751	1751	type	True	100.0	954	955	95	conclusive
Acidipropionibacterium jensenii	strain=DSM 20535	GCA_000425285.1	1749	1749	type	True	85.7873	713	955	95	below_threshold
Acidipropionibacterium acidipropionici	strain=CGMCC 1.2230	GCA_001441165.1	1748	1748	type	True	82.161	618	955	95	below_threshold
Acidipropionibacterium acidipropionici	strain=DSM 4900	GCA_000427845.1	1748	1748	type	True	82.1135	597	955	95	below_threshold
Acidipropionibacterium virtanenii	strain=JS278	GCA_003325455.1	2057246	2057246	type	True	81.68	565	955	95	below_threshold
Cutibacterium granulosum	strain=NCTC11865	GCA_900186975.1	33011	33011	type	True	79.163	269	955	95	below_threshold
Cutibacterium granulosum	strain=DSM 20700	GCA_000463665.1	33011	33011	type	True	78.8708	207	955	95	below_threshold
Propionibacterium australiense	strain=NML98A072	GCA_003666605.1	119981	119981	type	True	77.9691	189	955	95	below_threshold
Propionibacterium australiense	strain=NCTC13651	GCA_900637915.1	119981	119981	type	True	77.8431	195	955	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	76.7772	182	955	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.5301	159	955	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	76.3532	137	955	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	76.1403	165	955	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	75.8148	196	955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:01,553] [INFO] DFAST Taxonomy check result was written to GCF_000423445.1_ASM42344v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:01,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:01,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:01,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg969906c6-801c-4510-9270-b6b76f02628e/dqc_reference/checkm_data
[2024-01-24 13:29:01,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:01,589] [INFO] Task started: CheckM
[2024-01-24 13:29:01,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423445.1_ASM42344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423445.1_ASM42344v1_genomic.fna/checkm_input GCF_000423445.1_ASM42344v1_genomic.fna/checkm_result
[2024-01-24 13:29:47,734] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:47,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:47,752] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:47,753] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:47,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423445.1_ASM42344v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:47,753] [INFO] Task started: Blastn
[2024-01-24 13:29:47,754] [INFO] Running command: blastn -query GCF_000423445.1_ASM42344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg969906c6-801c-4510-9270-b6b76f02628e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423445.1_ASM42344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:49,369] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:49,373] [INFO] Selected 10 target genomes.
[2024-01-24 13:29:49,373] [INFO] Target genome list was writen to GCF_000423445.1_ASM42344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:49,381] [INFO] Task started: fastANI
[2024-01-24 13:29:49,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg6485b970-8dbf-4e4f-b19f-4e43929bc63c/GCF_000423445.1_ASM42344v1_genomic.fna.gz --refList GCF_000423445.1_ASM42344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423445.1_ASM42344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:56,216] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:56,225] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:56,225] [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_000423445.1	s__Acidipropionibacterium thoenii	100.0	953	955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000425285.1	s__Acidipropionibacterium jensenii	85.7812	713	955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	98.58	97.66	0.92	0.89	5	-
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	82.1708	617	955	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	81.6928	564	955	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	79.8645	408	955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186975.1	s__Cutibacterium granulosum	79.1702	270	955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	98.45	97.35	0.97	0.94	5	-
GCF_003666605.1	s__Propionibacterium australiense	77.9691	189	955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.91	99.75	0.98	0.97	4	-
GCA_002387005.1	s__Luteococcus avicola	77.7982	184	955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Luteococcus	95.0	96.77	96.77	0.82	0.82	2	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.6354	242	955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_002899455.1	s__Streptomyces sp002899455	76.098	183	955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:56,227] [INFO] GTDB search result was written to GCF_000423445.1_ASM42344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:56,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:56,230] [INFO] DFAST_QC result json was written to GCF_000423445.1_ASM42344v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:56,231] [INFO] DFAST_QC completed!
[2024-01-24 13:29:56,231] [INFO] Total running time: 0h1m16s