[2024-01-24 13:36:32,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f3de360-e0a8-4c94-ae4c-d24f521e0b78/dqc_reference
[2024-01-24 13:36:33,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,639] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg84f7ad14-f32e-4890-9b9c-0bccc519f651/GCF_000425285.1_ASM42528v1_genomic.fna.gz | prodigal -d GCF_000425285.1_ASM42528v1_genomic.fna/cds.fna -a GCF_000425285.1_ASM42528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:42,416] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:42,416] [INFO] Task started: HMMsearch
[2024-01-24 13:36:42,416] [INFO] Running command: hmmsearch --tblout GCF_000425285.1_ASM42528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f3de360-e0a8-4c94-ae4c-d24f521e0b78/dqc_reference/reference_markers.hmm GCF_000425285.1_ASM42528v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:42,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:42,655] [INFO] Found 6/6 markers.
[2024-01-24 13:36:42,684] [INFO] Query marker FASTA was written to GCF_000425285.1_ASM42528v1_genomic.fna/markers.fasta
[2024-01-24 13:36:42,685] [INFO] Task started: Blastn
[2024-01-24 13:36:42,685] [INFO] Running command: blastn -query GCF_000425285.1_ASM42528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f3de360-e0a8-4c94-ae4c-d24f521e0b78/dqc_reference/reference_markers.fasta -out GCF_000425285.1_ASM42528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:43,693] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:43,696] [INFO] Selected 11 target genomes.
[2024-01-24 13:36:43,697] [INFO] Target genome list was writen to GCF_000425285.1_ASM42528v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:43,705] [INFO] Task started: fastANI
[2024-01-24 13:36:43,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f7ad14-f32e-4890-9b9c-0bccc519f651/GCF_000425285.1_ASM42528v1_genomic.fna.gz --refList GCF_000425285.1_ASM42528v1_genomic.fna/target_genomes.txt --output GCF_000425285.1_ASM42528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:53,051] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:53,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f3de360-e0a8-4c94-ae4c-d24f521e0b78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:53,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f3de360-e0a8-4c94-ae4c-d24f521e0b78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:53,066] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:53,066] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:53,066] [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 jensenii	strain=DSM 20535	GCA_000425285.1	1749	1749	type	True	100.0	978	981	95	conclusive
Acidipropionibacterium thoenii	strain=DSM 20276	GCA_000423445.1	1751	1751	type	True	85.7988	718	981	95	below_threshold
Acidipropionibacterium acidipropionici	strain=CGMCC 1.2230	GCA_001441165.1	1748	1748	type	True	82.7555	675	981	95	below_threshold
Acidipropionibacterium acidipropionici	strain=DSM 4900	GCA_000427845.1	1748	1748	type	True	82.7462	666	981	95	below_threshold
Acidipropionibacterium virtanenii	strain=JS278	GCA_003325455.1	2057246	2057246	type	True	82.3805	614	981	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.5887	241	981	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	76.3979	176	981	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	76.0933	136	981	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	75.9131	222	981	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	75.8666	164	981	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	75.7738	209	981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:53,068] [INFO] DFAST Taxonomy check result was written to GCF_000425285.1_ASM42528v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:53,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:53,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:53,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f3de360-e0a8-4c94-ae4c-d24f521e0b78/dqc_reference/checkm_data
[2024-01-24 13:36:53,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:53,101] [INFO] Task started: CheckM
[2024-01-24 13:36:53,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425285.1_ASM42528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425285.1_ASM42528v1_genomic.fna/checkm_input GCF_000425285.1_ASM42528v1_genomic.fna/checkm_result
[2024-01-24 13:37:41,984] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:41,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:42,000] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:42,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:42,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425285.1_ASM42528v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:42,002] [INFO] Task started: Blastn
[2024-01-24 13:37:42,002] [INFO] Running command: blastn -query GCF_000425285.1_ASM42528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f3de360-e0a8-4c94-ae4c-d24f521e0b78/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425285.1_ASM42528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:43,607] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:43,610] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:43,611] [INFO] Target genome list was writen to GCF_000425285.1_ASM42528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:43,618] [INFO] Task started: fastANI
[2024-01-24 13:37:43,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f7ad14-f32e-4890-9b9c-0bccc519f651/GCF_000425285.1_ASM42528v1_genomic.fna.gz --refList GCF_000425285.1_ASM42528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425285.1_ASM42528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:48,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:48,688] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:48,688] [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_000425285.1	s__Acidipropionibacterium jensenii	100.0	978	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	98.58	97.66	0.92	0.89	5	conclusive
GCF_000423445.1	s__Acidipropionibacterium thoenii	85.7936	719	981	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	82.7404	678	981	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	82.3337	618	981	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	80.4558	437	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.8724	253	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_014164775.1	s__Arachnia sp014164775	77.4051	212	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.46	97.46	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:48,690] [INFO] GTDB search result was written to GCF_000425285.1_ASM42528v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:48,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:48,693] [INFO] DFAST_QC result json was written to GCF_000425285.1_ASM42528v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:48,693] [INFO] DFAST_QC completed!
[2024-01-24 13:37:48,693] [INFO] Total running time: 0h1m16s