[2023-06-30 23:36:32,758] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:36:32,761] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:36:32,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg38887279-ccfe-4f69-995e-baf24e644ddb/dqc_reference
[2023-06-30 23:36:33,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:36:34,000] [INFO] Task started: Prodigal
[2023-06-30 23:36:34,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg3367b250-c148-4b2d-8eef-eb62b1591c19/GCA_900762165.1_SRS1170746_5_genomic.fna.gz | prodigal -d GCA_900762165.1_SRS1170746_5_genomic.fna/cds.fna -a GCA_900762165.1_SRS1170746_5_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:36:37,926] [INFO] Task succeeded: Prodigal
[2023-06-30 23:36:37,927] [INFO] Task started: HMMsearch
[2023-06-30 23:36:37,927] [INFO] Running command: hmmsearch --tblout GCA_900762165.1_SRS1170746_5_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38887279-ccfe-4f69-995e-baf24e644ddb/dqc_reference/reference_markers.hmm GCA_900762165.1_SRS1170746_5_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:36:38,173] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:36:38,175] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3367b250-c148-4b2d-8eef-eb62b1591c19/GCA_900762165.1_SRS1170746_5_genomic.fna.gz]
[2023-06-30 23:36:38,203] [INFO] Query marker FASTA was written to GCA_900762165.1_SRS1170746_5_genomic.fna/markers.fasta
[2023-06-30 23:36:38,204] [INFO] Task started: Blastn
[2023-06-30 23:36:38,204] [INFO] Running command: blastn -query GCA_900762165.1_SRS1170746_5_genomic.fna/markers.fasta -db /var/lib/cwl/stg38887279-ccfe-4f69-995e-baf24e644ddb/dqc_reference/reference_markers.fasta -out GCA_900762165.1_SRS1170746_5_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:36:38,828] [INFO] Task succeeded: Blastn
[2023-06-30 23:36:38,832] [INFO] Selected 24 target genomes.
[2023-06-30 23:36:38,832] [INFO] Target genome list was writen to GCA_900762165.1_SRS1170746_5_genomic.fna/target_genomes.txt
[2023-06-30 23:36:38,837] [INFO] Task started: fastANI
[2023-06-30 23:36:38,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg3367b250-c148-4b2d-8eef-eb62b1591c19/GCA_900762165.1_SRS1170746_5_genomic.fna.gz --refList GCA_900762165.1_SRS1170746_5_genomic.fna/target_genomes.txt --output GCA_900762165.1_SRS1170746_5_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:36:54,611] [INFO] Task succeeded: fastANI
[2023-06-30 23:36:54,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38887279-ccfe-4f69-995e-baf24e644ddb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:36:54,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38887279-ccfe-4f69-995e-baf24e644ddb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:36:54,615] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 23:36:54,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 23:36:54,615] [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
Pradoshia eiseniae	strain=EAG3	GCA_002946355.1	2064768	2064768	type	True	98.8795	126	127	95	conclusive
--------------------------------------------------------------------------------
[2023-06-30 23:36:54,617] [INFO] DFAST Taxonomy check result was written to GCA_900762165.1_SRS1170746_5_genomic.fna/tc_result.tsv
[2023-06-30 23:36:54,618] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:36:54,618] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:36:54,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38887279-ccfe-4f69-995e-baf24e644ddb/dqc_reference/checkm_data
[2023-06-30 23:36:54,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:36:54,648] [INFO] Task started: CheckM
[2023-06-30 23:36:54,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900762165.1_SRS1170746_5_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900762165.1_SRS1170746_5_genomic.fna/checkm_input GCA_900762165.1_SRS1170746_5_genomic.fna/checkm_result
[2023-06-30 23:37:13,879] [INFO] Task succeeded: CheckM
[2023-06-30 23:37:13,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:37:13,905] [INFO] ===== Completeness check finished =====
[2023-06-30 23:37:13,906] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:37:13,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900762165.1_SRS1170746_5_genomic.fna/markers.fasta)
[2023-06-30 23:37:13,907] [INFO] Task started: Blastn
[2023-06-30 23:37:13,907] [INFO] Running command: blastn -query GCA_900762165.1_SRS1170746_5_genomic.fna/markers.fasta -db /var/lib/cwl/stg38887279-ccfe-4f69-995e-baf24e644ddb/dqc_reference/reference_markers_gtdb.fasta -out GCA_900762165.1_SRS1170746_5_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:37:14,769] [INFO] Task succeeded: Blastn
[2023-06-30 23:37:14,775] [INFO] Selected 18 target genomes.
[2023-06-30 23:37:14,775] [INFO] Target genome list was writen to GCA_900762165.1_SRS1170746_5_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:37:14,867] [INFO] Task started: fastANI
[2023-06-30 23:37:14,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg3367b250-c148-4b2d-8eef-eb62b1591c19/GCA_900762165.1_SRS1170746_5_genomic.fna.gz --refList GCA_900762165.1_SRS1170746_5_genomic.fna/target_genomes_gtdb.txt --output GCA_900762165.1_SRS1170746_5_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:37:26,547] [INFO] Task succeeded: fastANI
[2023-06-30 23:37:26,555] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:37:26,556] [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_002946355.1	s__Pradoshia eiseniae	98.8795	126	127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_904501845.1	s__Pradoshia sp904501845	86.8462	116	127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_001183965.1	s__Pradoshia sp001183965	83.5588	112	127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 23:37:26,558] [INFO] GTDB search result was written to GCA_900762165.1_SRS1170746_5_genomic.fna/result_gtdb.tsv
[2023-06-30 23:37:26,559] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:37:26,561] [INFO] DFAST_QC result json was written to GCA_900762165.1_SRS1170746_5_genomic.fna/dqc_result.json
[2023-06-30 23:37:26,562] [INFO] DFAST_QC completed!
[2023-06-30 23:37:26,562] [INFO] Total running time: 0h0m54s