[2023-06-27 11:49:11,970] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:49:11,972] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:49:11,972] [INFO] DQC Reference Directory: /var/lib/cwl/stgca03281b-f5c9-4eac-892d-be0f29498c6b/dqc_reference
[2023-06-27 11:49:13,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:49:13,159] [INFO] Task started: Prodigal
[2023-06-27 11:49:13,159] [INFO] Running command: gunzip -c /var/lib/cwl/stg28458ed7-39bd-4ff1-90f1-2600e8fec821/GCA_026985895.1_ASM2698589v1_genomic.fna.gz | prodigal -d GCA_026985895.1_ASM2698589v1_genomic.fna/cds.fna -a GCA_026985895.1_ASM2698589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:49:18,046] [INFO] Task succeeded: Prodigal
[2023-06-27 11:49:18,047] [INFO] Task started: HMMsearch
[2023-06-27 11:49:18,047] [INFO] Running command: hmmsearch --tblout GCA_026985895.1_ASM2698589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca03281b-f5c9-4eac-892d-be0f29498c6b/dqc_reference/reference_markers.hmm GCA_026985895.1_ASM2698589v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:49:18,241] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:49:18,242] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28458ed7-39bd-4ff1-90f1-2600e8fec821/GCA_026985895.1_ASM2698589v1_genomic.fna.gz]
[2023-06-27 11:49:18,312] [INFO] Query marker FASTA was written to GCA_026985895.1_ASM2698589v1_genomic.fna/markers.fasta
[2023-06-27 11:49:18,313] [INFO] Task started: Blastn
[2023-06-27 11:49:18,313] [INFO] Running command: blastn -query GCA_026985895.1_ASM2698589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca03281b-f5c9-4eac-892d-be0f29498c6b/dqc_reference/reference_markers.fasta -out GCA_026985895.1_ASM2698589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:49:18,957] [INFO] Task succeeded: Blastn
[2023-06-27 11:49:18,963] [INFO] Selected 27 target genomes.
[2023-06-27 11:49:18,963] [INFO] Target genome list was writen to GCA_026985895.1_ASM2698589v1_genomic.fna/target_genomes.txt
[2023-06-27 11:49:18,970] [INFO] Task started: fastANI
[2023-06-27 11:49:18,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg28458ed7-39bd-4ff1-90f1-2600e8fec821/GCA_026985895.1_ASM2698589v1_genomic.fna.gz --refList GCA_026985895.1_ASM2698589v1_genomic.fna/target_genomes.txt --output GCA_026985895.1_ASM2698589v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:49:36,652] [INFO] Task succeeded: fastANI
[2023-06-27 11:49:36,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca03281b-f5c9-4eac-892d-be0f29498c6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:49:36,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca03281b-f5c9-4eac-892d-be0f29498c6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:49:36,656] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:49:36,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:49:36,656] [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
Cocleimonas flava	strain=DSM 24830	GCA_004339015.1	634765	634765	type	True	77.3612	63	647	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:49:36,658] [INFO] DFAST Taxonomy check result was written to GCA_026985895.1_ASM2698589v1_genomic.fna/tc_result.tsv
[2023-06-27 11:49:36,658] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:49:36,658] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:49:36,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca03281b-f5c9-4eac-892d-be0f29498c6b/dqc_reference/checkm_data
[2023-06-27 11:49:36,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:49:36,688] [INFO] Task started: CheckM
[2023-06-27 11:49:36,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026985895.1_ASM2698589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026985895.1_ASM2698589v1_genomic.fna/checkm_input GCA_026985895.1_ASM2698589v1_genomic.fna/checkm_result
[2023-06-27 11:49:59,374] [INFO] Task succeeded: CheckM
[2023-06-27 11:49:59,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 17.99%
Strain heterogeneity: 3.85%
--------------------------------------------------------------------------------
[2023-06-27 11:49:59,410] [INFO] ===== Completeness check finished =====
[2023-06-27 11:49:59,410] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:49:59,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026985895.1_ASM2698589v1_genomic.fna/markers.fasta)
[2023-06-27 11:49:59,411] [INFO] Task started: Blastn
[2023-06-27 11:49:59,411] [INFO] Running command: blastn -query GCA_026985895.1_ASM2698589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca03281b-f5c9-4eac-892d-be0f29498c6b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026985895.1_ASM2698589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:50:00,233] [INFO] Task succeeded: Blastn
[2023-06-27 11:50:00,243] [INFO] Selected 26 target genomes.
[2023-06-27 11:50:00,243] [INFO] Target genome list was writen to GCA_026985895.1_ASM2698589v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:50:00,272] [INFO] Task started: fastANI
[2023-06-27 11:50:00,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg28458ed7-39bd-4ff1-90f1-2600e8fec821/GCA_026985895.1_ASM2698589v1_genomic.fna.gz --refList GCA_026985895.1_ASM2698589v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026985895.1_ASM2698589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:50:12,878] [INFO] Task succeeded: fastANI
[2023-06-27 11:50:12,883] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:50:12,884] [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_004339015.1	s__Cocleimonas flava	77.3612	63	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Cocleimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972955.1	s__Cocleimonas sp003972955	76.5111	65	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Cocleimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:50:12,902] [INFO] GTDB search result was written to GCA_026985895.1_ASM2698589v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:50:12,903] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:50:12,909] [INFO] DFAST_QC result json was written to GCA_026985895.1_ASM2698589v1_genomic.fna/dqc_result.json
[2023-06-27 11:50:12,910] [INFO] DFAST_QC completed!
[2023-06-27 11:50:12,910] [INFO] Total running time: 0h1m1s