[2024-01-24 12:53:36,653] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,655] [INFO] DQC Reference Directory: /var/lib/cwl/stge226fe0c-de30-41b1-bb4f-dc45bed2ae6e/dqc_reference
[2024-01-24 12:53:39,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:39,884] [INFO] Task started: Prodigal
[2024-01-24 12:53:39,885] [INFO] Running command: gunzip -c /var/lib/cwl/stg56b4885f-8948-45fb-a201-4673ae3be1bb/GCF_000495435.3_ASM49543v3_genomic.fna.gz | prodigal -d GCF_000495435.3_ASM49543v3_genomic.fna/cds.fna -a GCF_000495435.3_ASM49543v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:49,712] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:49,712] [INFO] Task started: HMMsearch
[2024-01-24 12:53:49,712] [INFO] Running command: hmmsearch --tblout GCF_000495435.3_ASM49543v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge226fe0c-de30-41b1-bb4f-dc45bed2ae6e/dqc_reference/reference_markers.hmm GCF_000495435.3_ASM49543v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:50,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:50,048] [INFO] Found 6/6 markers.
[2024-01-24 12:53:50,085] [INFO] Query marker FASTA was written to GCF_000495435.3_ASM49543v3_genomic.fna/markers.fasta
[2024-01-24 12:53:50,086] [INFO] Task started: Blastn
[2024-01-24 12:53:50,086] [INFO] Running command: blastn -query GCF_000495435.3_ASM49543v3_genomic.fna/markers.fasta -db /var/lib/cwl/stge226fe0c-de30-41b1-bb4f-dc45bed2ae6e/dqc_reference/reference_markers.fasta -out GCF_000495435.3_ASM49543v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:51,267] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:51,271] [INFO] Selected 20 target genomes.
[2024-01-24 12:53:51,272] [INFO] Target genome list was writen to GCF_000495435.3_ASM49543v3_genomic.fna/target_genomes.txt
[2024-01-24 12:53:51,280] [INFO] Task started: fastANI
[2024-01-24 12:53:51,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b4885f-8948-45fb-a201-4673ae3be1bb/GCF_000495435.3_ASM49543v3_genomic.fna.gz --refList GCF_000495435.3_ASM49543v3_genomic.fna/target_genomes.txt --output GCF_000495435.3_ASM49543v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:05,082] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:05,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge226fe0c-de30-41b1-bb4f-dc45bed2ae6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:05,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge226fe0c-de30-41b1-bb4f-dc45bed2ae6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:05,121] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:05,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:05,121] [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
Youngiibacter fragilis	strain=232.1	GCA_000495435.3	1408819	1408819	type	True	100.0	1209	1212	95	conclusive
Youngiibacter multivorans	strain=DSM 6139	GCA_017873395.1	937251	937251	type	True	85.2114	910	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:05,123] [INFO] DFAST Taxonomy check result was written to GCF_000495435.3_ASM49543v3_genomic.fna/tc_result.tsv
[2024-01-24 12:54:05,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:05,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:05,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge226fe0c-de30-41b1-bb4f-dc45bed2ae6e/dqc_reference/checkm_data
[2024-01-24 12:54:05,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:05,170] [INFO] Task started: CheckM
[2024-01-24 12:54:05,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000495435.3_ASM49543v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000495435.3_ASM49543v3_genomic.fna/checkm_input GCF_000495435.3_ASM49543v3_genomic.fna/checkm_result
[2024-01-24 12:54:38,431] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:38,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:38,453] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:38,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:38,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000495435.3_ASM49543v3_genomic.fna/markers.fasta)
[2024-01-24 12:54:38,455] [INFO] Task started: Blastn
[2024-01-24 12:54:38,455] [INFO] Running command: blastn -query GCF_000495435.3_ASM49543v3_genomic.fna/markers.fasta -db /var/lib/cwl/stge226fe0c-de30-41b1-bb4f-dc45bed2ae6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000495435.3_ASM49543v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:39,311] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:39,316] [INFO] Selected 14 target genomes.
[2024-01-24 12:54:39,316] [INFO] Target genome list was writen to GCF_000495435.3_ASM49543v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:39,344] [INFO] Task started: fastANI
[2024-01-24 12:54:39,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b4885f-8948-45fb-a201-4673ae3be1bb/GCF_000495435.3_ASM49543v3_genomic.fna.gz --refList GCF_000495435.3_ASM49543v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000495435.3_ASM49543v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:47,392] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:47,406] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:47,406] [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_000495435.3	s__Youngiibacter fragilis	100.0	1209	1212	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Youngiibacter	95.0	99.98	99.96	0.97	0.96	4	conclusive
GCA_002428605.1	s__Youngiibacter sp002428605	87.6641	739	1212	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Youngiibacter	95.0	98.57	98.51	0.82	0.82	3	-
GCF_017873395.1	s__Youngiibacter multivorans	85.1998	911	1212	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Youngiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428415.1	s__Youngiibacter sp002428415	84.5227	730	1212	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Youngiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:47,408] [INFO] GTDB search result was written to GCF_000495435.3_ASM49543v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:47,409] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:47,412] [INFO] DFAST_QC result json was written to GCF_000495435.3_ASM49543v3_genomic.fna/dqc_result.json
[2024-01-24 12:54:47,412] [INFO] DFAST_QC completed!
[2024-01-24 12:54:47,412] [INFO] Total running time: 0h1m11s