[2023-06-28 08:55:08,331] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:55:08,338] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:55:08,338] [INFO] DQC Reference Directory: /var/lib/cwl/stg09a06dd4-a8b1-4aa4-a71f-64a87243c895/dqc_reference
[2023-06-28 08:55:10,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:55:10,281] [INFO] Task started: Prodigal
[2023-06-28 08:55:10,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg19b3d604-83cc-4cd7-b138-fe2ff04a5a91/GCA_017650795.1_ASM1765079v1_genomic.fna.gz | prodigal -d GCA_017650795.1_ASM1765079v1_genomic.fna/cds.fna -a GCA_017650795.1_ASM1765079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:55:13,183] [INFO] Task succeeded: Prodigal
[2023-06-28 08:55:13,184] [INFO] Task started: HMMsearch
[2023-06-28 08:55:13,184] [INFO] Running command: hmmsearch --tblout GCA_017650795.1_ASM1765079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09a06dd4-a8b1-4aa4-a71f-64a87243c895/dqc_reference/reference_markers.hmm GCA_017650795.1_ASM1765079v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:55:13,387] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:55:13,388] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg19b3d604-83cc-4cd7-b138-fe2ff04a5a91/GCA_017650795.1_ASM1765079v1_genomic.fna.gz]
[2023-06-28 08:55:13,411] [INFO] Query marker FASTA was written to GCA_017650795.1_ASM1765079v1_genomic.fna/markers.fasta
[2023-06-28 08:55:13,411] [INFO] Task started: Blastn
[2023-06-28 08:55:13,411] [INFO] Running command: blastn -query GCA_017650795.1_ASM1765079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09a06dd4-a8b1-4aa4-a71f-64a87243c895/dqc_reference/reference_markers.fasta -out GCA_017650795.1_ASM1765079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:55:14,345] [INFO] Task succeeded: Blastn
[2023-06-28 08:55:14,349] [INFO] Selected 18 target genomes.
[2023-06-28 08:55:14,349] [INFO] Target genome list was writen to GCA_017650795.1_ASM1765079v1_genomic.fna/target_genomes.txt
[2023-06-28 08:55:14,377] [INFO] Task started: fastANI
[2023-06-28 08:55:14,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b3d604-83cc-4cd7-b138-fe2ff04a5a91/GCA_017650795.1_ASM1765079v1_genomic.fna.gz --refList GCA_017650795.1_ASM1765079v1_genomic.fna/target_genomes.txt --output GCA_017650795.1_ASM1765079v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:55:21,315] [INFO] Task succeeded: fastANI
[2023-06-28 08:55:21,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09a06dd4-a8b1-4aa4-a71f-64a87243c895/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:55:21,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09a06dd4-a8b1-4aa4-a71f-64a87243c895/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:55:21,319] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:55:21,319] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:55:21,319] [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
--------------------------------------------------------------------------------
[2023-06-28 08:55:21,321] [INFO] DFAST Taxonomy check result was written to GCA_017650795.1_ASM1765079v1_genomic.fna/tc_result.tsv
[2023-06-28 08:55:21,322] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:55:21,322] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:55:21,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09a06dd4-a8b1-4aa4-a71f-64a87243c895/dqc_reference/checkm_data
[2023-06-28 08:55:21,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:55:21,349] [INFO] Task started: CheckM
[2023-06-28 08:55:21,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017650795.1_ASM1765079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017650795.1_ASM1765079v1_genomic.fna/checkm_input GCA_017650795.1_ASM1765079v1_genomic.fna/checkm_result
[2023-06-28 08:55:38,509] [INFO] Task succeeded: CheckM
[2023-06-28 08:55:38,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:55:38,530] [INFO] ===== Completeness check finished =====
[2023-06-28 08:55:38,530] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:55:38,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017650795.1_ASM1765079v1_genomic.fna/markers.fasta)
[2023-06-28 08:55:38,531] [INFO] Task started: Blastn
[2023-06-28 08:55:38,531] [INFO] Running command: blastn -query GCA_017650795.1_ASM1765079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09a06dd4-a8b1-4aa4-a71f-64a87243c895/dqc_reference/reference_markers_gtdb.fasta -out GCA_017650795.1_ASM1765079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:55:39,364] [INFO] Task succeeded: Blastn
[2023-06-28 08:55:39,368] [INFO] Selected 21 target genomes.
[2023-06-28 08:55:39,368] [INFO] Target genome list was writen to GCA_017650795.1_ASM1765079v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:55:39,396] [INFO] Task started: fastANI
[2023-06-28 08:55:39,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b3d604-83cc-4cd7-b138-fe2ff04a5a91/GCA_017650795.1_ASM1765079v1_genomic.fna.gz --refList GCA_017650795.1_ASM1765079v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017650795.1_ASM1765079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:55:44,756] [INFO] Task succeeded: fastANI
[2023-06-28 08:55:44,765] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:55:44,766] [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_017650795.1	s__HGM11367 sp017650795	100.0	355	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__HGM11367	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015069385.1	s__HGM11367 sp015069385	78.0614	57	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__HGM11367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767835.1	s__HGM11367 sp900767835	77.8182	54	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__HGM11367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015069335.1	s__HGM11367 sp015069335	77.6051	51	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__HGM11367	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:55:44,768] [INFO] GTDB search result was written to GCA_017650795.1_ASM1765079v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:55:44,768] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:55:44,771] [INFO] DFAST_QC result json was written to GCA_017650795.1_ASM1765079v1_genomic.fna/dqc_result.json
[2023-06-28 08:55:44,771] [INFO] DFAST_QC completed!
[2023-06-28 08:55:44,771] [INFO] Total running time: 0h0m36s