[2023-06-28 06:09:43,463] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:09:43,466] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:09:43,466] [INFO] DQC Reference Directory: /var/lib/cwl/stgf79d1d7c-f780-4edc-937c-bc3b26608865/dqc_reference
[2023-06-28 06:09:45,984] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:09:45,992] [INFO] Task started: Prodigal
[2023-06-28 06:09:45,992] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf371ea3-9486-4ae7-bb1a-ce15356e19f7/GCA_002708465.1_ASM270846v1_genomic.fna.gz | prodigal -d GCA_002708465.1_ASM270846v1_genomic.fna/cds.fna -a GCA_002708465.1_ASM270846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:09:52,028] [INFO] Task succeeded: Prodigal
[2023-06-28 06:09:52,028] [INFO] Task started: HMMsearch
[2023-06-28 06:09:52,029] [INFO] Running command: hmmsearch --tblout GCA_002708465.1_ASM270846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf79d1d7c-f780-4edc-937c-bc3b26608865/dqc_reference/reference_markers.hmm GCA_002708465.1_ASM270846v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:09:52,253] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:09:52,254] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdf371ea3-9486-4ae7-bb1a-ce15356e19f7/GCA_002708465.1_ASM270846v1_genomic.fna.gz]
[2023-06-28 06:09:52,284] [INFO] Query marker FASTA was written to GCA_002708465.1_ASM270846v1_genomic.fna/markers.fasta
[2023-06-28 06:09:52,284] [INFO] Task started: Blastn
[2023-06-28 06:09:52,284] [INFO] Running command: blastn -query GCA_002708465.1_ASM270846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf79d1d7c-f780-4edc-937c-bc3b26608865/dqc_reference/reference_markers.fasta -out GCA_002708465.1_ASM270846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:09:53,003] [INFO] Task succeeded: Blastn
[2023-06-28 06:09:53,011] [INFO] Selected 10 target genomes.
[2023-06-28 06:09:53,011] [INFO] Target genome list was writen to GCA_002708465.1_ASM270846v1_genomic.fna/target_genomes.txt
[2023-06-28 06:09:53,025] [INFO] Task started: fastANI
[2023-06-28 06:09:53,025] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf371ea3-9486-4ae7-bb1a-ce15356e19f7/GCA_002708465.1_ASM270846v1_genomic.fna.gz --refList GCA_002708465.1_ASM270846v1_genomic.fna/target_genomes.txt --output GCA_002708465.1_ASM270846v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:10:00,217] [INFO] Task succeeded: fastANI
[2023-06-28 06:10:00,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf79d1d7c-f780-4edc-937c-bc3b26608865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:10:00,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf79d1d7c-f780-4edc-937c-bc3b26608865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:10:00,220] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:10:00,220] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 06:10:00,220] [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
--------------------------------------------------------------------------------
[2023-06-28 06:10:00,222] [INFO] DFAST Taxonomy check result was written to GCA_002708465.1_ASM270846v1_genomic.fna/tc_result.tsv
[2023-06-28 06:10:00,223] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:10:00,223] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:10:00,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf79d1d7c-f780-4edc-937c-bc3b26608865/dqc_reference/checkm_data
[2023-06-28 06:10:00,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:10:00,286] [INFO] Task started: CheckM
[2023-06-28 06:10:00,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708465.1_ASM270846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708465.1_ASM270846v1_genomic.fna/checkm_input GCA_002708465.1_ASM270846v1_genomic.fna/checkm_result
[2023-06-28 06:10:27,099] [INFO] Task succeeded: CheckM
[2023-06-28 06:10:27,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:10:27,128] [INFO] ===== Completeness check finished =====
[2023-06-28 06:10:27,128] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:10:27,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708465.1_ASM270846v1_genomic.fna/markers.fasta)
[2023-06-28 06:10:27,129] [INFO] Task started: Blastn
[2023-06-28 06:10:27,129] [INFO] Running command: blastn -query GCA_002708465.1_ASM270846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf79d1d7c-f780-4edc-937c-bc3b26608865/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708465.1_ASM270846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:10:27,984] [INFO] Task succeeded: Blastn
[2023-06-28 06:10:27,990] [INFO] Selected 10 target genomes.
[2023-06-28 06:10:27,990] [INFO] Target genome list was writen to GCA_002708465.1_ASM270846v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:10:27,997] [INFO] Task started: fastANI
[2023-06-28 06:10:27,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf371ea3-9486-4ae7-bb1a-ce15356e19f7/GCA_002708465.1_ASM270846v1_genomic.fna.gz --refList GCA_002708465.1_ASM270846v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708465.1_ASM270846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:10:34,623] [INFO] Task succeeded: fastANI
[2023-06-28 06:10:34,628] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:10:34,629] [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_002708465.1	s__UBA8108 sp002708465	100.0	787	793	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	95.06	95.06	0.65	0.65	2	conclusive
GCA_002320775.1	s__UBA8108 sp002320775	91.7103	681	793	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695115.1	s__UBA8108 sp002695115	81.328	408	793	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	98.97	98.97	0.70	0.70	2	-
--------------------------------------------------------------------------------
[2023-06-28 06:10:34,631] [INFO] GTDB search result was written to GCA_002708465.1_ASM270846v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:10:34,631] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:10:34,634] [INFO] DFAST_QC result json was written to GCA_002708465.1_ASM270846v1_genomic.fna/dqc_result.json
[2023-06-28 06:10:34,634] [INFO] DFAST_QC completed!
[2023-06-28 06:10:34,634] [INFO] Total running time: 0h0m51s