[2023-06-30 09:12:43,001] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:12:43,006] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:12:43,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9fec14c-8ffc-4b3b-a25e-df261ae44456/dqc_reference
[2023-06-30 09:12:44,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:12:44,599] [INFO] Task started: Prodigal
[2023-06-30 09:12:44,600] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6298867-8a26-427d-b515-e41197225eca/GCA_900769005.1_SRS476193_2_genomic.fna.gz | prodigal -d GCA_900769005.1_SRS476193_2_genomic.fna/cds.fna -a GCA_900769005.1_SRS476193_2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:12:56,390] [INFO] Task succeeded: Prodigal
[2023-06-30 09:12:56,391] [INFO] Task started: HMMsearch
[2023-06-30 09:12:56,391] [INFO] Running command: hmmsearch --tblout GCA_900769005.1_SRS476193_2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9fec14c-8ffc-4b3b-a25e-df261ae44456/dqc_reference/reference_markers.hmm GCA_900769005.1_SRS476193_2_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:12:56,629] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:12:56,631] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb6298867-8a26-427d-b515-e41197225eca/GCA_900769005.1_SRS476193_2_genomic.fna.gz]
[2023-06-30 09:12:56,659] [INFO] Query marker FASTA was written to GCA_900769005.1_SRS476193_2_genomic.fna/markers.fasta
[2023-06-30 09:12:56,660] [INFO] Task started: Blastn
[2023-06-30 09:12:56,660] [INFO] Running command: blastn -query GCA_900769005.1_SRS476193_2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9fec14c-8ffc-4b3b-a25e-df261ae44456/dqc_reference/reference_markers.fasta -out GCA_900769005.1_SRS476193_2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:12:57,256] [INFO] Task succeeded: Blastn
[2023-06-30 09:12:57,260] [INFO] Selected 28 target genomes.
[2023-06-30 09:12:57,261] [INFO] Target genome list was writen to GCA_900769005.1_SRS476193_2_genomic.fna/target_genomes.txt
[2023-06-30 09:12:57,262] [INFO] Task started: fastANI
[2023-06-30 09:12:57,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6298867-8a26-427d-b515-e41197225eca/GCA_900769005.1_SRS476193_2_genomic.fna.gz --refList GCA_900769005.1_SRS476193_2_genomic.fna/target_genomes.txt --output GCA_900769005.1_SRS476193_2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:13:10,764] [INFO] Task succeeded: fastANI
[2023-06-30 09:13:10,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9fec14c-8ffc-4b3b-a25e-df261ae44456/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:13:10,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9fec14c-8ffc-4b3b-a25e-df261ae44456/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:13:10,767] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:13:10,767] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 09:13:10,768] [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
--------------------------------------------------------------------------------
[2023-06-30 09:13:10,770] [INFO] DFAST Taxonomy check result was written to GCA_900769005.1_SRS476193_2_genomic.fna/tc_result.tsv
[2023-06-30 09:13:10,771] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:13:10,771] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:13:10,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9fec14c-8ffc-4b3b-a25e-df261ae44456/dqc_reference/checkm_data
[2023-06-30 09:13:10,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:13:10,804] [INFO] Task started: CheckM
[2023-06-30 09:13:10,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900769005.1_SRS476193_2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900769005.1_SRS476193_2_genomic.fna/checkm_input GCA_900769005.1_SRS476193_2_genomic.fna/checkm_result
[2023-06-30 09:13:47,309] [INFO] Task succeeded: CheckM
[2023-06-30 09:13:47,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 9.26%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-30 09:13:47,336] [INFO] ===== Completeness check finished =====
[2023-06-30 09:13:47,337] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:13:47,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900769005.1_SRS476193_2_genomic.fna/markers.fasta)
[2023-06-30 09:13:47,338] [INFO] Task started: Blastn
[2023-06-30 09:13:47,338] [INFO] Running command: blastn -query GCA_900769005.1_SRS476193_2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9fec14c-8ffc-4b3b-a25e-df261ae44456/dqc_reference/reference_markers_gtdb.fasta -out GCA_900769005.1_SRS476193_2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:13:48,261] [INFO] Task succeeded: Blastn
[2023-06-30 09:13:48,265] [INFO] Selected 20 target genomes.
[2023-06-30 09:13:48,265] [INFO] Target genome list was writen to GCA_900769005.1_SRS476193_2_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:13:48,270] [INFO] Task started: fastANI
[2023-06-30 09:13:48,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6298867-8a26-427d-b515-e41197225eca/GCA_900769005.1_SRS476193_2_genomic.fna.gz --refList GCA_900769005.1_SRS476193_2_genomic.fna/target_genomes_gtdb.txt --output GCA_900769005.1_SRS476193_2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:13:54,519] [INFO] Task succeeded: fastANI
[2023-06-30 09:13:54,527] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 09:13:54,527] [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_016297215.1	s__RF16 sp016297215	93.244	121	148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766775.1	s__RF16 sp900766775	92.3332	118	148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768725.1	s__RF16 sp900768725	90.4722	96	148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 09:13:54,530] [INFO] GTDB search result was written to GCA_900769005.1_SRS476193_2_genomic.fna/result_gtdb.tsv
[2023-06-30 09:13:54,531] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:13:54,533] [INFO] DFAST_QC result json was written to GCA_900769005.1_SRS476193_2_genomic.fna/dqc_result.json
[2023-06-30 09:13:54,533] [INFO] DFAST_QC completed!
[2023-06-30 09:13:54,533] [INFO] Total running time: 0h1m12s