[2024-01-25 19:00:50,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:50,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:50,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg030215d5-cca0-4ffb-8c0d-f197fe81f6f4/dqc_reference
[2024-01-25 19:00:51,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:51,690] [INFO] Task started: Prodigal
[2024-01-25 19:00:51,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c3f91c2-147a-4ae3-a32b-445ecc73fe86/GCF_003030305.1_ASM303030v1_genomic.fna.gz | prodigal -d GCF_003030305.1_ASM303030v1_genomic.fna/cds.fna -a GCF_003030305.1_ASM303030v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:58,646] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:58,646] [INFO] Task started: HMMsearch
[2024-01-25 19:00:58,646] [INFO] Running command: hmmsearch --tblout GCF_003030305.1_ASM303030v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg030215d5-cca0-4ffb-8c0d-f197fe81f6f4/dqc_reference/reference_markers.hmm GCF_003030305.1_ASM303030v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:58,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:58,826] [INFO] Found 6/6 markers.
[2024-01-25 19:00:58,847] [INFO] Query marker FASTA was written to GCF_003030305.1_ASM303030v1_genomic.fna/markers.fasta
[2024-01-25 19:00:58,847] [INFO] Task started: Blastn
[2024-01-25 19:00:58,847] [INFO] Running command: blastn -query GCF_003030305.1_ASM303030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg030215d5-cca0-4ffb-8c0d-f197fe81f6f4/dqc_reference/reference_markers.fasta -out GCF_003030305.1_ASM303030v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:59,588] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:59,591] [INFO] Selected 10 target genomes.
[2024-01-25 19:00:59,591] [INFO] Target genome list was writen to GCF_003030305.1_ASM303030v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:59,601] [INFO] Task started: fastANI
[2024-01-25 19:00:59,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c3f91c2-147a-4ae3-a32b-445ecc73fe86/GCF_003030305.1_ASM303030v1_genomic.fna.gz --refList GCF_003030305.1_ASM303030v1_genomic.fna/target_genomes.txt --output GCF_003030305.1_ASM303030v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:08,222] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:08,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg030215d5-cca0-4ffb-8c0d-f197fe81f6f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:08,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg030215d5-cca0-4ffb-8c0d-f197fe81f6f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:08,229] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:01:08,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:08,229] [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 acnes	strain=ATCC 6919	GCA_003030305.1	1747	1747	type	True	100.0	830	831	95	conclusive
Cutibacterium acnes	strain=DSM 1897	GCA_004136195.1	1747	1747	type	True	99.9995	830	831	95	conclusive
Cutibacterium acnes	strain=ATCC 6919	GCA_008728435.1	1747	1747	type	True	99.998	829	831	95	conclusive
Cutibacterium acnes	strain=DSM 1897	GCA_000472405.1	1747	1747	type	True	99.9942	819	831	95	conclusive
Cutibacterium acnes	strain=ATCC 6919	GCA_000730485.1	1747	1747	type	True	99.9456	778	831	95	conclusive
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.0448	56	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:08,230] [INFO] DFAST Taxonomy check result was written to GCF_003030305.1_ASM303030v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:08,231] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:08,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:08,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg030215d5-cca0-4ffb-8c0d-f197fe81f6f4/dqc_reference/checkm_data
[2024-01-25 19:01:08,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:08,258] [INFO] Task started: CheckM
[2024-01-25 19:01:08,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003030305.1_ASM303030v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003030305.1_ASM303030v1_genomic.fna/checkm_input GCF_003030305.1_ASM303030v1_genomic.fna/checkm_result
[2024-01-25 19:01:33,550] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:33,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:33,571] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:33,571] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:33,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003030305.1_ASM303030v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:33,571] [INFO] Task started: Blastn
[2024-01-25 19:01:33,571] [INFO] Running command: blastn -query GCF_003030305.1_ASM303030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg030215d5-cca0-4ffb-8c0d-f197fe81f6f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003030305.1_ASM303030v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:34,699] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:34,705] [INFO] Selected 6 target genomes.
[2024-01-25 19:01:34,705] [INFO] Target genome list was writen to GCF_003030305.1_ASM303030v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:34,710] [INFO] Task started: fastANI
[2024-01-25 19:01:34,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c3f91c2-147a-4ae3-a32b-445ecc73fe86/GCF_003030305.1_ASM303030v1_genomic.fna.gz --refList GCF_003030305.1_ASM303030v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003030305.1_ASM303030v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:38,542] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:38,547] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:38,547] [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_003030305.1	s__Cutibacterium acnes	100.0	830	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.06	96.60	0.98	0.92	326	conclusive
GCF_001642025.1	s__Cutibacterium namnetense	88.3008	699	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.52	99.43	0.97	0.94	5	-
GCF_008326345.1	s__Cutibacterium modestum	85.9123	721	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.93	99.74	1.00	0.99	9	-
GCF_009696315.1	s__Cutibacterium porci	82.7122	613	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227295.1	s__Cutibacterium avidum	81.5782	581	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	97.99	95.78	0.94	0.87	29	-
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	78.4396	216	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:38,549] [INFO] GTDB search result was written to GCF_003030305.1_ASM303030v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:38,549] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:38,552] [INFO] DFAST_QC result json was written to GCF_003030305.1_ASM303030v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:38,552] [INFO] DFAST_QC completed!
[2024-01-25 19:01:38,552] [INFO] Total running time: 0h0m48s