[2024-01-25 17:40:05,519] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:05,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:05,523] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8bcdd92-fb7e-4bba-870a-5c08224c4b60/dqc_reference
[2024-01-25 17:40:06,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:06,655] [INFO] Task started: Prodigal
[2024-01-25 17:40:06,656] [INFO] Running command: gunzip -c /var/lib/cwl/stgae50655d-1078-4ae9-bb1c-99ef3c8bbabd/GCF_009909615.1_ASM990961v1_genomic.fna.gz | prodigal -d GCF_009909615.1_ASM990961v1_genomic.fna/cds.fna -a GCF_009909615.1_ASM990961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:17,604] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:17,604] [INFO] Task started: HMMsearch
[2024-01-25 17:40:17,604] [INFO] Running command: hmmsearch --tblout GCF_009909615.1_ASM990961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8bcdd92-fb7e-4bba-870a-5c08224c4b60/dqc_reference/reference_markers.hmm GCF_009909615.1_ASM990961v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:17,809] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:17,810] [INFO] Found 6/6 markers.
[2024-01-25 17:40:17,837] [INFO] Query marker FASTA was written to GCF_009909615.1_ASM990961v1_genomic.fna/markers.fasta
[2024-01-25 17:40:17,837] [INFO] Task started: Blastn
[2024-01-25 17:40:17,837] [INFO] Running command: blastn -query GCF_009909615.1_ASM990961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8bcdd92-fb7e-4bba-870a-5c08224c4b60/dqc_reference/reference_markers.fasta -out GCF_009909615.1_ASM990961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:18,394] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:18,397] [INFO] Selected 25 target genomes.
[2024-01-25 17:40:18,397] [INFO] Target genome list was writen to GCF_009909615.1_ASM990961v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:18,446] [INFO] Task started: fastANI
[2024-01-25 17:40:18,447] [INFO] Running command: fastANI --query /var/lib/cwl/stgae50655d-1078-4ae9-bb1c-99ef3c8bbabd/GCF_009909615.1_ASM990961v1_genomic.fna.gz --refList GCF_009909615.1_ASM990961v1_genomic.fna/target_genomes.txt --output GCF_009909615.1_ASM990961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:32,951] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:32,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8bcdd92-fb7e-4bba-870a-5c08224c4b60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:32,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8bcdd92-fb7e-4bba-870a-5c08224c4b60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:32,954] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:32,955] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:32,955] [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
Acidiluteibacter ferrifornacis	strain=S-15	GCA_009909615.1	2692424	2692424	type	True	100.0	1160	1162	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:40:32,956] [INFO] DFAST Taxonomy check result was written to GCF_009909615.1_ASM990961v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:32,956] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:32,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:32,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8bcdd92-fb7e-4bba-870a-5c08224c4b60/dqc_reference/checkm_data
[2024-01-25 17:40:32,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:32,993] [INFO] Task started: CheckM
[2024-01-25 17:40:32,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009909615.1_ASM990961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009909615.1_ASM990961v1_genomic.fna/checkm_input GCF_009909615.1_ASM990961v1_genomic.fna/checkm_result
[2024-01-25 17:41:07,982] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:07,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:08,018] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:08,018] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:08,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009909615.1_ASM990961v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:08,019] [INFO] Task started: Blastn
[2024-01-25 17:41:08,019] [INFO] Running command: blastn -query GCF_009909615.1_ASM990961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8bcdd92-fb7e-4bba-870a-5c08224c4b60/dqc_reference/reference_markers_gtdb.fasta -out GCF_009909615.1_ASM990961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:08,970] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:08,974] [INFO] Selected 22 target genomes.
[2024-01-25 17:41:08,974] [INFO] Target genome list was writen to GCF_009909615.1_ASM990961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:09,000] [INFO] Task started: fastANI
[2024-01-25 17:41:09,000] [INFO] Running command: fastANI --query /var/lib/cwl/stgae50655d-1078-4ae9-bb1c-99ef3c8bbabd/GCF_009909615.1_ASM990961v1_genomic.fna.gz --refList GCF_009909615.1_ASM990961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009909615.1_ASM990961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:21,111] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:21,115] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:21,115] [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_009909615.1	s__Acidiluteibacter ferrifornacis	100.0	1160	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Acidiluteibacter	95.0	97.97	97.97	0.91	0.91	2	conclusive
GCA_018402765.1	s__Acidiluteibacter sp018402765	78.8479	266	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Acidiluteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013112545.1	s__BCD18 sp013112545	77.1387	84	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BCD18	95.0	99.98	99.95	0.99	0.99	3	-
GCA_016763995.1	s__NORP294 sp016763995	75.8402	50	1162	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:21,117] [INFO] GTDB search result was written to GCF_009909615.1_ASM990961v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:21,117] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:21,119] [INFO] DFAST_QC result json was written to GCF_009909615.1_ASM990961v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:21,119] [INFO] DFAST_QC completed!
[2024-01-25 17:41:21,119] [INFO] Total running time: 0h1m16s