[2024-01-25 18:02:05,570] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:05,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:05,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg916cdb67-2a26-4d20-9d11-65442386bd4a/dqc_reference
[2024-01-25 18:02:06,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:06,712] [INFO] Task started: Prodigal
[2024-01-25 18:02:06,712] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3ca96b3-06d0-465a-a985-a254b04f6712/GCF_017873395.1_ASM1787339v1_genomic.fna.gz | prodigal -d GCF_017873395.1_ASM1787339v1_genomic.fna/cds.fna -a GCF_017873395.1_ASM1787339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:14,505] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:14,505] [INFO] Task started: HMMsearch
[2024-01-25 18:02:14,505] [INFO] Running command: hmmsearch --tblout GCF_017873395.1_ASM1787339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg916cdb67-2a26-4d20-9d11-65442386bd4a/dqc_reference/reference_markers.hmm GCF_017873395.1_ASM1787339v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:14,729] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:14,730] [INFO] Found 6/6 markers.
[2024-01-25 18:02:14,758] [INFO] Query marker FASTA was written to GCF_017873395.1_ASM1787339v1_genomic.fna/markers.fasta
[2024-01-25 18:02:14,759] [INFO] Task started: Blastn
[2024-01-25 18:02:14,759] [INFO] Running command: blastn -query GCF_017873395.1_ASM1787339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg916cdb67-2a26-4d20-9d11-65442386bd4a/dqc_reference/reference_markers.fasta -out GCF_017873395.1_ASM1787339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:15,300] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:15,302] [INFO] Selected 22 target genomes.
[2024-01-25 18:02:15,303] [INFO] Target genome list was writen to GCF_017873395.1_ASM1787339v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:15,337] [INFO] Task started: fastANI
[2024-01-25 18:02:15,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3ca96b3-06d0-465a-a985-a254b04f6712/GCF_017873395.1_ASM1787339v1_genomic.fna.gz --refList GCF_017873395.1_ASM1787339v1_genomic.fna/target_genomes.txt --output GCF_017873395.1_ASM1787339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:28,457] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:28,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg916cdb67-2a26-4d20-9d11-65442386bd4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:28,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg916cdb67-2a26-4d20-9d11-65442386bd4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:28,462] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:28,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:28,462] [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 multivorans	strain=DSM 6139	GCA_017873395.1	937251	937251	type	True	100.0	1184	1188	95	conclusive
Youngiibacter fragilis	strain=232.1	GCA_000495435.3	1408819	1408819	type	True	85.4605	891	1188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:28,464] [INFO] DFAST Taxonomy check result was written to GCF_017873395.1_ASM1787339v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:28,464] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:28,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:28,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg916cdb67-2a26-4d20-9d11-65442386bd4a/dqc_reference/checkm_data
[2024-01-25 18:02:28,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:28,504] [INFO] Task started: CheckM
[2024-01-25 18:02:28,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873395.1_ASM1787339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873395.1_ASM1787339v1_genomic.fna/checkm_input GCF_017873395.1_ASM1787339v1_genomic.fna/checkm_result
[2024-01-25 18:02:56,430] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:56,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:56,461] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:56,461] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:56,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873395.1_ASM1787339v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:56,462] [INFO] Task started: Blastn
[2024-01-25 18:02:56,462] [INFO] Running command: blastn -query GCF_017873395.1_ASM1787339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg916cdb67-2a26-4d20-9d11-65442386bd4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873395.1_ASM1787339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:57,298] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:57,300] [INFO] Selected 14 target genomes.
[2024-01-25 18:02:57,300] [INFO] Target genome list was writen to GCF_017873395.1_ASM1787339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:57,316] [INFO] Task started: fastANI
[2024-01-25 18:02:57,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3ca96b3-06d0-465a-a985-a254b04f6712/GCF_017873395.1_ASM1787339v1_genomic.fna.gz --refList GCF_017873395.1_ASM1787339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873395.1_ASM1787339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:04,842] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:04,846] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:04,846] [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_017873395.1	s__Youngiibacter multivorans	100.0	1184	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Youngiibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002428415.1	s__Youngiibacter sp002428415	90.2742	776	1188	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_002428605.1	s__Youngiibacter sp002428605	86.443	732	1188	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_000495435.3	s__Youngiibacter fragilis	85.4411	893	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Youngiibacter	95.0	99.98	99.96	0.97	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:04,848] [INFO] GTDB search result was written to GCF_017873395.1_ASM1787339v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:04,848] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:04,851] [INFO] DFAST_QC result json was written to GCF_017873395.1_ASM1787339v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:04,851] [INFO] DFAST_QC completed!
[2024-01-25 18:03:04,851] [INFO] Total running time: 0h0m59s