[2024-01-24 13:08:58,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,011] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,011] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9c13fef-4901-4db1-87c6-009641e42ee3/dqc_reference
[2024-01-24 13:08:59,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,237] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg06de121c-aff0-4b1b-8df0-dcef3d9daea7/GCF_004340205.1_ASM434020v1_genomic.fna.gz | prodigal -d GCF_004340205.1_ASM434020v1_genomic.fna/cds.fna -a GCF_004340205.1_ASM434020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:15,698] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:15,699] [INFO] Task started: HMMsearch
[2024-01-24 13:09:15,699] [INFO] Running command: hmmsearch --tblout GCF_004340205.1_ASM434020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9c13fef-4901-4db1-87c6-009641e42ee3/dqc_reference/reference_markers.hmm GCF_004340205.1_ASM434020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:15,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:15,967] [INFO] Found 6/6 markers.
[2024-01-24 13:09:16,001] [INFO] Query marker FASTA was written to GCF_004340205.1_ASM434020v1_genomic.fna/markers.fasta
[2024-01-24 13:09:16,002] [INFO] Task started: Blastn
[2024-01-24 13:09:16,002] [INFO] Running command: blastn -query GCF_004340205.1_ASM434020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9c13fef-4901-4db1-87c6-009641e42ee3/dqc_reference/reference_markers.fasta -out GCF_004340205.1_ASM434020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:16,602] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:16,606] [INFO] Selected 28 target genomes.
[2024-01-24 13:09:16,606] [INFO] Target genome list was writen to GCF_004340205.1_ASM434020v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:16,682] [INFO] Task started: fastANI
[2024-01-24 13:09:16,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg06de121c-aff0-4b1b-8df0-dcef3d9daea7/GCF_004340205.1_ASM434020v1_genomic.fna.gz --refList GCF_004340205.1_ASM434020v1_genomic.fna/target_genomes.txt --output GCF_004340205.1_ASM434020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:34,508] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:34,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9c13fef-4901-4db1-87c6-009641e42ee3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:34,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9c13fef-4901-4db1-87c6-009641e42ee3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:34,516] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:34,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:34,516] [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
Acetobacteroides hydrogenigenes	strain=RL-C	GCA_004340205.1	979970	979970	type	True	100.0	1273	1274	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:09:34,517] [INFO] DFAST Taxonomy check result was written to GCF_004340205.1_ASM434020v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:34,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:34,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:34,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9c13fef-4901-4db1-87c6-009641e42ee3/dqc_reference/checkm_data
[2024-01-24 13:09:34,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:34,566] [INFO] Task started: CheckM
[2024-01-24 13:09:34,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340205.1_ASM434020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340205.1_ASM434020v1_genomic.fna/checkm_input GCF_004340205.1_ASM434020v1_genomic.fna/checkm_result
[2024-01-24 13:10:22,133] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:22,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:22,153] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:22,153] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:22,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340205.1_ASM434020v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:22,154] [INFO] Task started: Blastn
[2024-01-24 13:10:22,154] [INFO] Running command: blastn -query GCF_004340205.1_ASM434020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9c13fef-4901-4db1-87c6-009641e42ee3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340205.1_ASM434020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:22,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:22,974] [INFO] Selected 23 target genomes.
[2024-01-24 13:10:22,974] [INFO] Target genome list was writen to GCF_004340205.1_ASM434020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:23,049] [INFO] Task started: fastANI
[2024-01-24 13:10:23,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg06de121c-aff0-4b1b-8df0-dcef3d9daea7/GCF_004340205.1_ASM434020v1_genomic.fna.gz --refList GCF_004340205.1_ASM434020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340205.1_ASM434020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:34,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:34,776] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:34,776] [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_004340205.1	s__Acetobacteroides hydrogenigenes	100.0	1273	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ZOR0009;g__Acetobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000798815.1	s__Acetobacteroides sp000798815	79.0794	333	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ZOR0009;g__Acetobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:34,778] [INFO] GTDB search result was written to GCF_004340205.1_ASM434020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:34,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:34,781] [INFO] DFAST_QC result json was written to GCF_004340205.1_ASM434020v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:34,781] [INFO] DFAST_QC completed!
[2024-01-24 13:10:34,781] [INFO] Total running time: 0h1m37s