[2024-01-24 13:32:18,660] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg167ceddc-ddc4-4a37-bcb7-9bd0079e8636/dqc_reference
[2024-01-24 13:32:20,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:20,051] [INFO] Task started: Prodigal
[2024-01-24 13:32:20,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg12ade91b-bce3-42c3-8c2b-a2239e6f0316/GCF_009695905.1_ASM969590v1_genomic.fna.gz | prodigal -d GCF_009695905.1_ASM969590v1_genomic.fna/cds.fna -a GCF_009695905.1_ASM969590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:25,848] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:25,849] [INFO] Task started: HMMsearch
[2024-01-24 13:32:25,849] [INFO] Running command: hmmsearch --tblout GCF_009695905.1_ASM969590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg167ceddc-ddc4-4a37-bcb7-9bd0079e8636/dqc_reference/reference_markers.hmm GCF_009695905.1_ASM969590v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:26,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:26,111] [INFO] Found 6/6 markers.
[2024-01-24 13:32:26,131] [INFO] Query marker FASTA was written to GCF_009695905.1_ASM969590v1_genomic.fna/markers.fasta
[2024-01-24 13:32:26,131] [INFO] Task started: Blastn
[2024-01-24 13:32:26,131] [INFO] Running command: blastn -query GCF_009695905.1_ASM969590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg167ceddc-ddc4-4a37-bcb7-9bd0079e8636/dqc_reference/reference_markers.fasta -out GCF_009695905.1_ASM969590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:26,754] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:26,758] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:26,758] [INFO] Target genome list was writen to GCF_009695905.1_ASM969590v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:26,767] [INFO] Task started: fastANI
[2024-01-24 13:32:26,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg12ade91b-bce3-42c3-8c2b-a2239e6f0316/GCF_009695905.1_ASM969590v1_genomic.fna.gz --refList GCF_009695905.1_ASM969590v1_genomic.fna/target_genomes.txt --output GCF_009695905.1_ASM969590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:34,218] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:34,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg167ceddc-ddc4-4a37-bcb7-9bd0079e8636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:34,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg167ceddc-ddc4-4a37-bcb7-9bd0079e8636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:34,227] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:34,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:34,228] [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
Mogibacterium kristiansenii	strain=WCA-MUC-591-APC-4B	GCA_009695905.1	2606708	2606708	type	True	100.0	661	663	95	conclusive
Mogibacterium timidum	strain=ATCC 33093	GCA_000525775.1	35519	35519	type	True	78.101	51	663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:34,230] [INFO] DFAST Taxonomy check result was written to GCF_009695905.1_ASM969590v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:34,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:34,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:34,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg167ceddc-ddc4-4a37-bcb7-9bd0079e8636/dqc_reference/checkm_data
[2024-01-24 13:32:34,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:34,260] [INFO] Task started: CheckM
[2024-01-24 13:32:34,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695905.1_ASM969590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695905.1_ASM969590v1_genomic.fna/checkm_input GCF_009695905.1_ASM969590v1_genomic.fna/checkm_result
[2024-01-24 13:32:58,272] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:58,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,293] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:58,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:58,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695905.1_ASM969590v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:58,294] [INFO] Task started: Blastn
[2024-01-24 13:32:58,294] [INFO] Running command: blastn -query GCF_009695905.1_ASM969590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg167ceddc-ddc4-4a37-bcb7-9bd0079e8636/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695905.1_ASM969590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:59,209] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:59,213] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:59,213] [INFO] Target genome list was writen to GCF_009695905.1_ASM969590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:59,258] [INFO] Task started: fastANI
[2024-01-24 13:32:59,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg12ade91b-bce3-42c3-8c2b-a2239e6f0316/GCF_009695905.1_ASM969590v1_genomic.fna.gz --refList GCF_009695905.1_ASM969590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695905.1_ASM969590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:05,471] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:05,476] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:05,476] [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_009695905.1	s__VUNA01 sp002299625	100.0	661	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01	95.0	97.61	96.13	0.91	0.86	6	conclusive
GCA_016775335.1	s__VUNA01 sp016775335	93.1571	537	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000525775.1	s__Mogibacterium timidum	78.101	51	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	98.94	98.78	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:05,481] [INFO] GTDB search result was written to GCF_009695905.1_ASM969590v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:05,481] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:05,483] [INFO] DFAST_QC result json was written to GCF_009695905.1_ASM969590v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:05,483] [INFO] DFAST_QC completed!
[2024-01-24 13:33:05,484] [INFO] Total running time: 0h0m47s