[2023-06-28 18:41:05,975] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:41:05,977] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:41:05,977] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0270e13-2653-4296-bd03-2896565aabdd/dqc_reference
[2023-06-28 18:41:07,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:41:07,195] [INFO] Task started: Prodigal
[2023-06-28 18:41:07,195] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ab21b1f-b214-4467-bc0d-9a67a997088d/GCA_017965205.1_ASM1796520v1_genomic.fna.gz | prodigal -d GCA_017965205.1_ASM1796520v1_genomic.fna/cds.fna -a GCA_017965205.1_ASM1796520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:41:10,979] [INFO] Task succeeded: Prodigal
[2023-06-28 18:41:10,979] [INFO] Task started: HMMsearch
[2023-06-28 18:41:10,979] [INFO] Running command: hmmsearch --tblout GCA_017965205.1_ASM1796520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0270e13-2653-4296-bd03-2896565aabdd/dqc_reference/reference_markers.hmm GCA_017965205.1_ASM1796520v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:41:11,192] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:41:11,194] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4ab21b1f-b214-4467-bc0d-9a67a997088d/GCA_017965205.1_ASM1796520v1_genomic.fna.gz]
[2023-06-28 18:41:11,221] [INFO] Query marker FASTA was written to GCA_017965205.1_ASM1796520v1_genomic.fna/markers.fasta
[2023-06-28 18:41:11,221] [INFO] Task started: Blastn
[2023-06-28 18:41:11,221] [INFO] Running command: blastn -query GCA_017965205.1_ASM1796520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0270e13-2653-4296-bd03-2896565aabdd/dqc_reference/reference_markers.fasta -out GCA_017965205.1_ASM1796520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:11,747] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:11,752] [INFO] Selected 25 target genomes.
[2023-06-28 18:41:11,752] [INFO] Target genome list was writen to GCA_017965205.1_ASM1796520v1_genomic.fna/target_genomes.txt
[2023-06-28 18:41:11,753] [INFO] Task started: fastANI
[2023-06-28 18:41:11,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ab21b1f-b214-4467-bc0d-9a67a997088d/GCA_017965205.1_ASM1796520v1_genomic.fna.gz --refList GCA_017965205.1_ASM1796520v1_genomic.fna/target_genomes.txt --output GCA_017965205.1_ASM1796520v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:41:31,374] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:31,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0270e13-2653-4296-bd03-2896565aabdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:41:31,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0270e13-2653-4296-bd03-2896565aabdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:41:31,376] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:41:31,377] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:41:31,377] [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 18:41:31,379] [INFO] DFAST Taxonomy check result was written to GCA_017965205.1_ASM1796520v1_genomic.fna/tc_result.tsv
[2023-06-28 18:41:31,380] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:41:31,380] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:41:31,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0270e13-2653-4296-bd03-2896565aabdd/dqc_reference/checkm_data
[2023-06-28 18:41:31,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:41:31,408] [INFO] Task started: CheckM
[2023-06-28 18:41:31,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017965205.1_ASM1796520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017965205.1_ASM1796520v1_genomic.fna/checkm_input GCA_017965205.1_ASM1796520v1_genomic.fna/checkm_result
[2023-06-28 18:41:50,227] [INFO] Task succeeded: CheckM
[2023-06-28 18:41:50,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.63%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 18:41:50,254] [INFO] ===== Completeness check finished =====
[2023-06-28 18:41:50,255] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:41:50,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017965205.1_ASM1796520v1_genomic.fna/markers.fasta)
[2023-06-28 18:41:50,255] [INFO] Task started: Blastn
[2023-06-28 18:41:50,256] [INFO] Running command: blastn -query GCA_017965205.1_ASM1796520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0270e13-2653-4296-bd03-2896565aabdd/dqc_reference/reference_markers_gtdb.fasta -out GCA_017965205.1_ASM1796520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:50,767] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:50,772] [INFO] Selected 8 target genomes.
[2023-06-28 18:41:50,772] [INFO] Target genome list was writen to GCA_017965205.1_ASM1796520v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:41:50,773] [INFO] Task started: fastANI
[2023-06-28 18:41:50,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ab21b1f-b214-4467-bc0d-9a67a997088d/GCA_017965205.1_ASM1796520v1_genomic.fna.gz --refList GCA_017965205.1_ASM1796520v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017965205.1_ASM1796520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:41:53,758] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:53,766] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:41:53,766] [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_017412505.1	s__RUG11894 sp017412505	87.0676	182	228	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	97.05	95.90	0.86	0.80	9	-
GCA_017619985.1	s__RUG11894 sp017619985	86.8494	176	228	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557505.1	s__RUG11894 sp017557505	85.4184	194	228	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626845.1	s__RUG11894 sp017626845	83.2128	174	228	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773665.1	s__RUG11894 sp902773665	83.1671	171	228	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	97.59	96.15	0.91	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-28 18:41:53,768] [INFO] GTDB search result was written to GCA_017965205.1_ASM1796520v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:41:53,769] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:41:53,771] [INFO] DFAST_QC result json was written to GCA_017965205.1_ASM1796520v1_genomic.fna/dqc_result.json
[2023-06-28 18:41:53,771] [INFO] DFAST_QC completed!
[2023-06-28 18:41:53,772] [INFO] Total running time: 0h0m48s