[2023-06-17 09:13:11,439] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:13:11,442] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:13:11,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg98f189e7-2fc1-41f1-bcff-9e35f8f476e4/dqc_reference
[2023-06-17 09:13:15,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:13:15,318] [INFO] Task started: Prodigal
[2023-06-17 09:13:15,319] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfe6b3d7-cdea-4397-a6c0-4af02fc24b61/GCA_028709265.1_ASM2870926v1_genomic.fna.gz | prodigal -d GCA_028709265.1_ASM2870926v1_genomic.fna/cds.fna -a GCA_028709265.1_ASM2870926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:13:17,953] [INFO] Task succeeded: Prodigal
[2023-06-17 09:13:17,953] [INFO] Task started: HMMsearch
[2023-06-17 09:13:17,953] [INFO] Running command: hmmsearch --tblout GCA_028709265.1_ASM2870926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98f189e7-2fc1-41f1-bcff-9e35f8f476e4/dqc_reference/reference_markers.hmm GCA_028709265.1_ASM2870926v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:13:18,268] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:13:18,270] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcfe6b3d7-cdea-4397-a6c0-4af02fc24b61/GCA_028709265.1_ASM2870926v1_genomic.fna.gz]
[2023-06-17 09:13:18,302] [INFO] Query marker FASTA was written to GCA_028709265.1_ASM2870926v1_genomic.fna/markers.fasta
[2023-06-17 09:13:18,303] [INFO] Task started: Blastn
[2023-06-17 09:13:18,303] [INFO] Running command: blastn -query GCA_028709265.1_ASM2870926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f189e7-2fc1-41f1-bcff-9e35f8f476e4/dqc_reference/reference_markers.fasta -out GCA_028709265.1_ASM2870926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:13:20,920] [INFO] Task succeeded: Blastn
[2023-06-17 09:13:20,924] [INFO] Selected 10 target genomes.
[2023-06-17 09:13:20,925] [INFO] Target genome list was writen to GCA_028709265.1_ASM2870926v1_genomic.fna/target_genomes.txt
[2023-06-17 09:13:20,932] [INFO] Task started: fastANI
[2023-06-17 09:13:20,932] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfe6b3d7-cdea-4397-a6c0-4af02fc24b61/GCA_028709265.1_ASM2870926v1_genomic.fna.gz --refList GCA_028709265.1_ASM2870926v1_genomic.fna/target_genomes.txt --output GCA_028709265.1_ASM2870926v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:13:26,656] [INFO] Task succeeded: fastANI
[2023-06-17 09:13:26,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98f189e7-2fc1-41f1-bcff-9e35f8f476e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:13:26,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98f189e7-2fc1-41f1-bcff-9e35f8f476e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:13:26,660] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:13:26,660] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 09:13:26,660] [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
--------------------------------------------------------------------------------
[2023-06-17 09:13:26,662] [INFO] DFAST Taxonomy check result was written to GCA_028709265.1_ASM2870926v1_genomic.fna/tc_result.tsv
[2023-06-17 09:13:26,663] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:13:26,663] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:13:26,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98f189e7-2fc1-41f1-bcff-9e35f8f476e4/dqc_reference/checkm_data
[2023-06-17 09:13:26,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:13:26,688] [INFO] Task started: CheckM
[2023-06-17 09:13:26,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028709265.1_ASM2870926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028709265.1_ASM2870926v1_genomic.fna/checkm_input GCA_028709265.1_ASM2870926v1_genomic.fna/checkm_result
[2023-06-17 09:13:43,640] [INFO] Task succeeded: CheckM
[2023-06-17 09:13:43,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:13:43,664] [INFO] ===== Completeness check finished =====
[2023-06-17 09:13:43,665] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:13:43,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028709265.1_ASM2870926v1_genomic.fna/markers.fasta)
[2023-06-17 09:13:43,665] [INFO] Task started: Blastn
[2023-06-17 09:13:43,666] [INFO] Running command: blastn -query GCA_028709265.1_ASM2870926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f189e7-2fc1-41f1-bcff-9e35f8f476e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_028709265.1_ASM2870926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:13:44,419] [INFO] Task succeeded: Blastn
[2023-06-17 09:13:44,423] [INFO] Selected 14 target genomes.
[2023-06-17 09:13:44,424] [INFO] Target genome list was writen to GCA_028709265.1_ASM2870926v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:13:44,434] [INFO] Task started: fastANI
[2023-06-17 09:13:44,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfe6b3d7-cdea-4397-a6c0-4af02fc24b61/GCA_028709265.1_ASM2870926v1_genomic.fna.gz --refList GCA_028709265.1_ASM2870926v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028709265.1_ASM2870926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:13:49,529] [INFO] Task succeeded: fastANI
[2023-06-17 09:13:49,535] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 09:13:49,535] [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_018402425.1	s__M30B28 sp018402425	78.4101	138	425	d__Bacteria;p__Atribacterota;c__JS1;o__SB-45;f__UBA6794;g__M30B28	95.0	98.57	98.46	0.71	0.68	3	-
GCA_002452835.1	s__UBA6794 sp002452835	77.0847	61	425	d__Bacteria;p__Atribacterota;c__JS1;o__SB-45;f__UBA6794;g__UBA6794	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 09:13:49,537] [INFO] GTDB search result was written to GCA_028709265.1_ASM2870926v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:13:49,538] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:13:49,540] [INFO] DFAST_QC result json was written to GCA_028709265.1_ASM2870926v1_genomic.fna/dqc_result.json
[2023-06-17 09:13:49,540] [INFO] DFAST_QC completed!
[2023-06-17 09:13:49,540] [INFO] Total running time: 0h0m38s