[2023-07-01 01:50:01,353] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:50:01,356] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:50:01,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg504b180f-b63f-4236-8340-78b8abdf1f23/dqc_reference
[2023-07-01 01:50:04,396] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:50:04,397] [INFO] Task started: Prodigal
[2023-07-01 01:50:04,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg05e8ab79-be02-4d29-8a9f-71608a1eff58/GCA_024742995.1_ASM2474299v1_genomic.fna.gz | prodigal -d GCA_024742995.1_ASM2474299v1_genomic.fna/cds.fna -a GCA_024742995.1_ASM2474299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:50:10,459] [INFO] Task succeeded: Prodigal
[2023-07-01 01:50:10,460] [INFO] Task started: HMMsearch
[2023-07-01 01:50:10,460] [INFO] Running command: hmmsearch --tblout GCA_024742995.1_ASM2474299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg504b180f-b63f-4236-8340-78b8abdf1f23/dqc_reference/reference_markers.hmm GCA_024742995.1_ASM2474299v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:50:10,704] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:50:10,705] [INFO] Found 6/6 markers.
[2023-07-01 01:50:10,736] [INFO] Query marker FASTA was written to GCA_024742995.1_ASM2474299v1_genomic.fna/markers.fasta
[2023-07-01 01:50:10,736] [INFO] Task started: Blastn
[2023-07-01 01:50:10,736] [INFO] Running command: blastn -query GCA_024742995.1_ASM2474299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg504b180f-b63f-4236-8340-78b8abdf1f23/dqc_reference/reference_markers.fasta -out GCA_024742995.1_ASM2474299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:50:12,146] [INFO] Task succeeded: Blastn
[2023-07-01 01:50:12,167] [INFO] Selected 33 target genomes.
[2023-07-01 01:50:12,168] [INFO] Target genome list was writen to GCA_024742995.1_ASM2474299v1_genomic.fna/target_genomes.txt
[2023-07-01 01:50:12,170] [INFO] Task started: fastANI
[2023-07-01 01:50:12,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg05e8ab79-be02-4d29-8a9f-71608a1eff58/GCA_024742995.1_ASM2474299v1_genomic.fna.gz --refList GCA_024742995.1_ASM2474299v1_genomic.fna/target_genomes.txt --output GCA_024742995.1_ASM2474299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:50:27,843] [INFO] Task succeeded: fastANI
[2023-07-01 01:50:27,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg504b180f-b63f-4236-8340-78b8abdf1f23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:50:27,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg504b180f-b63f-4236-8340-78b8abdf1f23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:50:27,847] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:50:27,847] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 01:50:27,847] [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
--------------------------------------------------------------------------------
[2023-07-01 01:50:27,850] [INFO] DFAST Taxonomy check result was written to GCA_024742995.1_ASM2474299v1_genomic.fna/tc_result.tsv
[2023-07-01 01:50:27,851] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:50:27,851] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:50:27,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg504b180f-b63f-4236-8340-78b8abdf1f23/dqc_reference/checkm_data
[2023-07-01 01:50:27,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:50:27,885] [INFO] Task started: CheckM
[2023-07-01 01:50:27,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024742995.1_ASM2474299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024742995.1_ASM2474299v1_genomic.fna/checkm_input GCA_024742995.1_ASM2474299v1_genomic.fna/checkm_result
[2023-07-01 01:50:52,821] [INFO] Task succeeded: CheckM
[2023-07-01 01:50:52,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:50:52,844] [INFO] ===== Completeness check finished =====
[2023-07-01 01:50:52,844] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:50:52,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024742995.1_ASM2474299v1_genomic.fna/markers.fasta)
[2023-07-01 01:50:52,845] [INFO] Task started: Blastn
[2023-07-01 01:50:52,845] [INFO] Running command: blastn -query GCA_024742995.1_ASM2474299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg504b180f-b63f-4236-8340-78b8abdf1f23/dqc_reference/reference_markers_gtdb.fasta -out GCA_024742995.1_ASM2474299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:50:53,863] [INFO] Task succeeded: Blastn
[2023-07-01 01:50:53,868] [INFO] Selected 29 target genomes.
[2023-07-01 01:50:53,868] [INFO] Target genome list was writen to GCA_024742995.1_ASM2474299v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:50:53,908] [INFO] Task started: fastANI
[2023-07-01 01:50:53,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg05e8ab79-be02-4d29-8a9f-71608a1eff58/GCA_024742995.1_ASM2474299v1_genomic.fna.gz --refList GCA_024742995.1_ASM2474299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024742995.1_ASM2474299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:51:07,243] [INFO] Task succeeded: fastANI
[2023-07-01 01:51:07,248] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 01:51:07,249] [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_002786165.1	s__GCA-2786165 sp002786165	77.3467	149	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__GCA-2786165	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877115.1	s__GCA-2786165 sp903877115	77.1845	87	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__GCA-2786165	95.0	97.95	97.95	0.80	0.80	2	-
GCA_903885895.1	s__GCA-2786165 sp903885895	76.36	89	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__GCA-2786165	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:51:07,265] [INFO] GTDB search result was written to GCA_024742995.1_ASM2474299v1_genomic.fna/result_gtdb.tsv
[2023-07-01 01:51:07,265] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:51:07,269] [INFO] DFAST_QC result json was written to GCA_024742995.1_ASM2474299v1_genomic.fna/dqc_result.json
[2023-07-01 01:51:07,269] [INFO] DFAST_QC completed!
[2023-07-01 01:51:07,270] [INFO] Total running time: 0h1m6s