[2023-06-29 14:18:14,005] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:18:14,007] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:18:14,007] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaa47a69-2668-4714-a0f8-c70b7c17aab2/dqc_reference
[2023-06-29 14:18:15,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:18:15,389] [INFO] Task started: Prodigal
[2023-06-29 14:18:15,389] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdee9929-8745-40b0-8e1e-09813795ccf7/GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna.gz | prodigal -d GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/cds.fna -a GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:18:22,127] [INFO] Task succeeded: Prodigal
[2023-06-29 14:18:22,128] [INFO] Task started: HMMsearch
[2023-06-29 14:18:22,128] [INFO] Running command: hmmsearch --tblout GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaa47a69-2668-4714-a0f8-c70b7c17aab2/dqc_reference/reference_markers.hmm GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:18:22,360] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:18:22,361] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbdee9929-8745-40b0-8e1e-09813795ccf7/GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna.gz]
[2023-06-29 14:18:22,393] [INFO] Query marker FASTA was written to GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/markers.fasta
[2023-06-29 14:18:22,394] [INFO] Task started: Blastn
[2023-06-29 14:18:22,394] [INFO] Running command: blastn -query GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaa47a69-2668-4714-a0f8-c70b7c17aab2/dqc_reference/reference_markers.fasta -out GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:18:23,023] [INFO] Task succeeded: Blastn
[2023-06-29 14:18:23,027] [INFO] Selected 24 target genomes.
[2023-06-29 14:18:23,027] [INFO] Target genome list was writen to GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/target_genomes.txt
[2023-06-29 14:18:23,033] [INFO] Task started: fastANI
[2023-06-29 14:18:23,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdee9929-8745-40b0-8e1e-09813795ccf7/GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna.gz --refList GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/target_genomes.txt --output GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:18:38,928] [INFO] Task succeeded: fastANI
[2023-06-29 14:18:38,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaa47a69-2668-4714-a0f8-c70b7c17aab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:18:38,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaa47a69-2668-4714-a0f8-c70b7c17aab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:18:38,934] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:18:38,935] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:18:38,935] [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
Amylibacter ulvae	strain=KCTC 32465	GCA_014652655.1	1651968	1651968	type	True	76.8791	108	629	95	below_threshold
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	76.7726	110	629	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:18:38,937] [INFO] DFAST Taxonomy check result was written to GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/tc_result.tsv
[2023-06-29 14:18:38,938] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:18:38,938] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:18:38,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaa47a69-2668-4714-a0f8-c70b7c17aab2/dqc_reference/checkm_data
[2023-06-29 14:18:38,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:18:38,971] [INFO] Task started: CheckM
[2023-06-29 14:18:38,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/checkm_input GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/checkm_result
[2023-06-29 14:19:04,371] [INFO] Task succeeded: CheckM
[2023-06-29 14:19:04,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:19:04,392] [INFO] ===== Completeness check finished =====
[2023-06-29 14:19:04,393] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:19:04,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/markers.fasta)
[2023-06-29 14:19:04,394] [INFO] Task started: Blastn
[2023-06-29 14:19:04,394] [INFO] Running command: blastn -query GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaa47a69-2668-4714-a0f8-c70b7c17aab2/dqc_reference/reference_markers_gtdb.fasta -out GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:19:05,211] [INFO] Task succeeded: Blastn
[2023-06-29 14:19:05,216] [INFO] Selected 27 target genomes.
[2023-06-29 14:19:05,216] [INFO] Target genome list was writen to GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:19:05,232] [INFO] Task started: fastANI
[2023-06-29 14:19:05,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdee9929-8745-40b0-8e1e-09813795ccf7/GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna.gz --refList GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/target_genomes_gtdb.txt --output GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:19:18,675] [INFO] Task succeeded: fastANI
[2023-06-29 14:19:18,683] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:19:18,683] [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_014652655.1	s__Amylibacter ulvae	76.8631	107	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184395.1	s__Amylibacter sp009184395	76.7917	60	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742285.1	s__Amylibacter kogurei	76.7726	110	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:19:18,685] [INFO] GTDB search result was written to GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:19:18,686] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:19:18,690] [INFO] DFAST_QC result json was written to GCA_937944065.1_L3_Bin_Bin_171_1_genomic.fna/dqc_result.json
[2023-06-29 14:19:18,690] [INFO] DFAST_QC completed!
[2023-06-29 14:19:18,690] [INFO] Total running time: 0h1m5s