[2024-01-24 11:34:40,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,837] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,838] [INFO] DQC Reference Directory: /var/lib/cwl/stgb06df385-027b-4c3c-b2d3-ccb0cc14af3f/dqc_reference
[2024-01-24 11:34:42,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,153] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb46f5a-4840-49f8-b184-3ad2d7541150/GCF_013285555.1_ASM1328555v1_genomic.fna.gz | prodigal -d GCF_013285555.1_ASM1328555v1_genomic.fna/cds.fna -a GCF_013285555.1_ASM1328555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:49,153] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:49,153] [INFO] Task started: HMMsearch
[2024-01-24 11:34:49,153] [INFO] Running command: hmmsearch --tblout GCF_013285555.1_ASM1328555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb06df385-027b-4c3c-b2d3-ccb0cc14af3f/dqc_reference/reference_markers.hmm GCF_013285555.1_ASM1328555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:49,434] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:49,435] [INFO] Found 6/6 markers.
[2024-01-24 11:34:49,464] [INFO] Query marker FASTA was written to GCF_013285555.1_ASM1328555v1_genomic.fna/markers.fasta
[2024-01-24 11:34:49,465] [INFO] Task started: Blastn
[2024-01-24 11:34:49,465] [INFO] Running command: blastn -query GCF_013285555.1_ASM1328555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb06df385-027b-4c3c-b2d3-ccb0cc14af3f/dqc_reference/reference_markers.fasta -out GCF_013285555.1_ASM1328555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:50,118] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:50,122] [INFO] Selected 20 target genomes.
[2024-01-24 11:34:50,122] [INFO] Target genome list was writen to GCF_013285555.1_ASM1328555v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:50,190] [INFO] Task started: fastANI
[2024-01-24 11:34:50,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb46f5a-4840-49f8-b184-3ad2d7541150/GCF_013285555.1_ASM1328555v1_genomic.fna.gz --refList GCF_013285555.1_ASM1328555v1_genomic.fna/target_genomes.txt --output GCF_013285555.1_ASM1328555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:01,854] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:01,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb06df385-027b-4c3c-b2d3-ccb0cc14af3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:01,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb06df385-027b-4c3c-b2d3-ccb0cc14af3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:01,859] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:01,859] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:01,859] [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	76.3708	82	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:01,860] [INFO] DFAST Taxonomy check result was written to GCF_013285555.1_ASM1328555v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:01,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:01,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:01,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb06df385-027b-4c3c-b2d3-ccb0cc14af3f/dqc_reference/checkm_data
[2024-01-24 11:35:01,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:01,893] [INFO] Task started: CheckM
[2024-01-24 11:35:01,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013285555.1_ASM1328555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013285555.1_ASM1328555v1_genomic.fna/checkm_input GCF_013285555.1_ASM1328555v1_genomic.fna/checkm_result
[2024-01-24 11:35:27,534] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:27,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:27,551] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:27,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:27,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013285555.1_ASM1328555v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:27,552] [INFO] Task started: Blastn
[2024-01-24 11:35:27,552] [INFO] Running command: blastn -query GCF_013285555.1_ASM1328555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb06df385-027b-4c3c-b2d3-ccb0cc14af3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013285555.1_ASM1328555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:28,593] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:28,596] [INFO] Selected 23 target genomes.
[2024-01-24 11:35:28,597] [INFO] Target genome list was writen to GCF_013285555.1_ASM1328555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:28,629] [INFO] Task started: fastANI
[2024-01-24 11:35:28,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb46f5a-4840-49f8-b184-3ad2d7541150/GCF_013285555.1_ASM1328555v1_genomic.fna.gz --refList GCF_013285555.1_ASM1328555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013285555.1_ASM1328555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:43,526] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:43,529] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:43,529] [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	99.9999	894	907	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	76.351	83	907	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 11:35:43,531] [INFO] GTDB search result was written to GCF_013285555.1_ASM1328555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:43,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:43,534] [INFO] DFAST_QC result json was written to GCF_013285555.1_ASM1328555v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:43,534] [INFO] DFAST_QC completed!
[2024-01-24 11:35:43,534] [INFO] Total running time: 0h1m3s