[2024-01-24 12:39:41,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg87fb3e75-5062-4ebc-bccd-42edea671d39/dqc_reference
[2024-01-24 12:39:42,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:42,887] [INFO] Task started: Prodigal
[2024-01-24 12:39:42,887] [INFO] Running command: gunzip -c /var/lib/cwl/stg394089de-0d49-43c8-83ad-eb74ee075159/GCF_013285545.1_ASM1328554v1_genomic.fna.gz | prodigal -d GCF_013285545.1_ASM1328554v1_genomic.fna/cds.fna -a GCF_013285545.1_ASM1328554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:50,283] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:50,284] [INFO] Task started: HMMsearch
[2024-01-24 12:39:50,284] [INFO] Running command: hmmsearch --tblout GCF_013285545.1_ASM1328554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87fb3e75-5062-4ebc-bccd-42edea671d39/dqc_reference/reference_markers.hmm GCF_013285545.1_ASM1328554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:50,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:50,541] [INFO] Found 6/6 markers.
[2024-01-24 12:39:50,570] [INFO] Query marker FASTA was written to GCF_013285545.1_ASM1328554v1_genomic.fna/markers.fasta
[2024-01-24 12:39:50,570] [INFO] Task started: Blastn
[2024-01-24 12:39:50,570] [INFO] Running command: blastn -query GCF_013285545.1_ASM1328554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87fb3e75-5062-4ebc-bccd-42edea671d39/dqc_reference/reference_markers.fasta -out GCF_013285545.1_ASM1328554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:51,240] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:51,244] [INFO] Selected 20 target genomes.
[2024-01-24 12:39:51,244] [INFO] Target genome list was writen to GCF_013285545.1_ASM1328554v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:51,251] [INFO] Task started: fastANI
[2024-01-24 12:39:51,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg394089de-0d49-43c8-83ad-eb74ee075159/GCF_013285545.1_ASM1328554v1_genomic.fna.gz --refList GCF_013285545.1_ASM1328554v1_genomic.fna/target_genomes.txt --output GCF_013285545.1_ASM1328554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:03,248] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:03,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87fb3e75-5062-4ebc-bccd-42edea671d39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:03,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87fb3e75-5062-4ebc-bccd-42edea671d39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:03,252] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:03,252] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:03,252] [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
Anthocerotibacter panamensis	strain=C109	GCA_018389385.1	2857077	2857077	type	True	76.2679	79	885	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:03,253] [INFO] DFAST Taxonomy check result was written to GCF_013285545.1_ASM1328554v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:03,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:03,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:03,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87fb3e75-5062-4ebc-bccd-42edea671d39/dqc_reference/checkm_data
[2024-01-24 12:40:03,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:03,290] [INFO] Task started: CheckM
[2024-01-24 12:40:03,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013285545.1_ASM1328554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013285545.1_ASM1328554v1_genomic.fna/checkm_input GCF_013285545.1_ASM1328554v1_genomic.fna/checkm_result
[2024-01-24 12:40:29,703] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:29,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:29,726] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:29,727] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:29,727] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013285545.1_ASM1328554v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:29,728] [INFO] Task started: Blastn
[2024-01-24 12:40:29,728] [INFO] Running command: blastn -query GCF_013285545.1_ASM1328554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87fb3e75-5062-4ebc-bccd-42edea671d39/dqc_reference/reference_markers_gtdb.fasta -out GCF_013285545.1_ASM1328554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:30,709] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:30,713] [INFO] Selected 23 target genomes.
[2024-01-24 12:40:30,714] [INFO] Target genome list was writen to GCF_013285545.1_ASM1328554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:31,311] [INFO] Task started: fastANI
[2024-01-24 12:40:31,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg394089de-0d49-43c8-83ad-eb74ee075159/GCF_013285545.1_ASM1328554v1_genomic.fna.gz --refList GCF_013285545.1_ASM1328554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013285545.1_ASM1328554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:46,584] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:46,591] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:46,591] [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
GCA_013285555.1	s__Aurora vandensis	99.9107	822	885	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__LV9;g__Aurora	95.0	99.91	99.91	0.93	0.93	2	conclusive
GCF_018389385.1	s__Anthocerotibacter panamensis	76.2679	79	885	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__LV9;g__Anthocerotibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:46,593] [INFO] GTDB search result was written to GCF_013285545.1_ASM1328554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:46,594] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:46,596] [INFO] DFAST_QC result json was written to GCF_013285545.1_ASM1328554v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:46,596] [INFO] DFAST_QC completed!
[2024-01-24 12:40:46,596] [INFO] Total running time: 0h1m5s