[2023-06-28 15:54:11,970] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:54:11,972] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:54:11,972] [INFO] DQC Reference Directory: /var/lib/cwl/stgab49cdb1-57e7-4a12-a0d1-f273f0ff76d5/dqc_reference
[2023-06-28 15:54:13,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:54:13,256] [INFO] Task started: Prodigal
[2023-06-28 15:54:13,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg38c75003-d62a-435f-875b-0fb3d66c62be/GCA_020440665.1_ASM2044066v1_genomic.fna.gz | prodigal -d GCA_020440665.1_ASM2044066v1_genomic.fna/cds.fna -a GCA_020440665.1_ASM2044066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:54:24,585] [INFO] Task succeeded: Prodigal
[2023-06-28 15:54:24,585] [INFO] Task started: HMMsearch
[2023-06-28 15:54:24,586] [INFO] Running command: hmmsearch --tblout GCA_020440665.1_ASM2044066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab49cdb1-57e7-4a12-a0d1-f273f0ff76d5/dqc_reference/reference_markers.hmm GCA_020440665.1_ASM2044066v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:54:24,804] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:54:24,805] [INFO] Found 6/6 markers.
[2023-06-28 15:54:24,835] [INFO] Query marker FASTA was written to GCA_020440665.1_ASM2044066v1_genomic.fna/markers.fasta
[2023-06-28 15:54:24,835] [INFO] Task started: Blastn
[2023-06-28 15:54:24,835] [INFO] Running command: blastn -query GCA_020440665.1_ASM2044066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab49cdb1-57e7-4a12-a0d1-f273f0ff76d5/dqc_reference/reference_markers.fasta -out GCA_020440665.1_ASM2044066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:54:25,406] [INFO] Task succeeded: Blastn
[2023-06-28 15:54:25,409] [INFO] Selected 16 target genomes.
[2023-06-28 15:54:25,410] [INFO] Target genome list was writen to GCA_020440665.1_ASM2044066v1_genomic.fna/target_genomes.txt
[2023-06-28 15:54:25,422] [INFO] Task started: fastANI
[2023-06-28 15:54:25,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c75003-d62a-435f-875b-0fb3d66c62be/GCA_020440665.1_ASM2044066v1_genomic.fna.gz --refList GCA_020440665.1_ASM2044066v1_genomic.fna/target_genomes.txt --output GCA_020440665.1_ASM2044066v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:54:38,190] [INFO] Task succeeded: fastANI
[2023-06-28 15:54:38,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab49cdb1-57e7-4a12-a0d1-f273f0ff76d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:54:38,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab49cdb1-57e7-4a12-a0d1-f273f0ff76d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:54:38,192] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:54:38,192] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 15:54:38,192] [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 15:54:38,193] [INFO] DFAST Taxonomy check result was written to GCA_020440665.1_ASM2044066v1_genomic.fna/tc_result.tsv
[2023-06-28 15:54:38,193] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:54:38,193] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:54:38,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab49cdb1-57e7-4a12-a0d1-f273f0ff76d5/dqc_reference/checkm_data
[2023-06-28 15:54:38,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:54:38,236] [INFO] Task started: CheckM
[2023-06-28 15:54:38,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020440665.1_ASM2044066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020440665.1_ASM2044066v1_genomic.fna/checkm_input GCA_020440665.1_ASM2044066v1_genomic.fna/checkm_result
[2023-06-28 15:55:12,982] [INFO] Task succeeded: CheckM
[2023-06-28 15:55:12,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:55:13,000] [INFO] ===== Completeness check finished =====
[2023-06-28 15:55:13,000] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:55:13,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020440665.1_ASM2044066v1_genomic.fna/markers.fasta)
[2023-06-28 15:55:13,001] [INFO] Task started: Blastn
[2023-06-28 15:55:13,001] [INFO] Running command: blastn -query GCA_020440665.1_ASM2044066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab49cdb1-57e7-4a12-a0d1-f273f0ff76d5/dqc_reference/reference_markers_gtdb.fasta -out GCA_020440665.1_ASM2044066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:55:13,874] [INFO] Task succeeded: Blastn
[2023-06-28 15:55:13,877] [INFO] Selected 21 target genomes.
[2023-06-28 15:55:13,877] [INFO] Target genome list was writen to GCA_020440665.1_ASM2044066v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:55:13,887] [INFO] Task started: fastANI
[2023-06-28 15:55:13,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c75003-d62a-435f-875b-0fb3d66c62be/GCA_020440665.1_ASM2044066v1_genomic.fna.gz --refList GCA_020440665.1_ASM2044066v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020440665.1_ASM2044066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:55:28,118] [INFO] Task succeeded: fastANI
[2023-06-28 15:55:28,121] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:55:28,121] [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_016932385.1	s__JAFGCY01 sp016932385	76.556	153	1277	d__Bacteria;p__4484-113;c__4484-113;o__4484-113;f__JAFGCY01;g__JAFGCY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262885.1	s__Pseudonocardia sp002262885	74.6597	55	1277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:55:28,123] [INFO] GTDB search result was written to GCA_020440665.1_ASM2044066v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:55:28,123] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:55:28,125] [INFO] DFAST_QC result json was written to GCA_020440665.1_ASM2044066v1_genomic.fna/dqc_result.json
[2023-06-28 15:55:28,125] [INFO] DFAST_QC completed!
[2023-06-28 15:55:28,125] [INFO] Total running time: 0h1m16s