[2023-06-17 08:21:45,231] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:21:45,234] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:21:45,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg182efeb7-b389-4a43-a111-58989ccf1040/dqc_reference
[2023-06-17 08:21:46,491] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:21:46,492] [INFO] Task started: Prodigal
[2023-06-17 08:21:46,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg1688ff12-ef59-428c-a7fe-e5f5180a76fc/GCA_009704345.1_ASM970434v1_genomic.fna.gz | prodigal -d GCA_009704345.1_ASM970434v1_genomic.fna/cds.fna -a GCA_009704345.1_ASM970434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:21:48,897] [INFO] Task succeeded: Prodigal
[2023-06-17 08:21:48,897] [INFO] Task started: HMMsearch
[2023-06-17 08:21:48,897] [INFO] Running command: hmmsearch --tblout GCA_009704345.1_ASM970434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg182efeb7-b389-4a43-a111-58989ccf1040/dqc_reference/reference_markers.hmm GCA_009704345.1_ASM970434v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:21:49,085] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:21:49,086] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1688ff12-ef59-428c-a7fe-e5f5180a76fc/GCA_009704345.1_ASM970434v1_genomic.fna.gz]
[2023-06-17 08:21:49,105] [INFO] Query marker FASTA was written to GCA_009704345.1_ASM970434v1_genomic.fna/markers.fasta
[2023-06-17 08:21:49,105] [INFO] Task started: Blastn
[2023-06-17 08:21:49,105] [INFO] Running command: blastn -query GCA_009704345.1_ASM970434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg182efeb7-b389-4a43-a111-58989ccf1040/dqc_reference/reference_markers.fasta -out GCA_009704345.1_ASM970434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:21:49,773] [INFO] Task succeeded: Blastn
[2023-06-17 08:21:49,778] [INFO] Selected 8 target genomes.
[2023-06-17 08:21:49,779] [INFO] Target genome list was writen to GCA_009704345.1_ASM970434v1_genomic.fna/target_genomes.txt
[2023-06-17 08:21:49,942] [INFO] Task started: fastANI
[2023-06-17 08:21:49,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg1688ff12-ef59-428c-a7fe-e5f5180a76fc/GCA_009704345.1_ASM970434v1_genomic.fna.gz --refList GCA_009704345.1_ASM970434v1_genomic.fna/target_genomes.txt --output GCA_009704345.1_ASM970434v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:21:52,365] [INFO] Task succeeded: fastANI
[2023-06-17 08:21:52,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg182efeb7-b389-4a43-a111-58989ccf1040/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:21:52,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg182efeb7-b389-4a43-a111-58989ccf1040/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:21:52,368] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:21:52,368] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 08:21:52,369] [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 08:21:52,372] [INFO] DFAST Taxonomy check result was written to GCA_009704345.1_ASM970434v1_genomic.fna/tc_result.tsv
[2023-06-17 08:21:52,372] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:21:52,373] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:21:52,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg182efeb7-b389-4a43-a111-58989ccf1040/dqc_reference/checkm_data
[2023-06-17 08:21:52,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:21:52,398] [INFO] Task started: CheckM
[2023-06-17 08:21:52,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009704345.1_ASM970434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009704345.1_ASM970434v1_genomic.fna/checkm_input GCA_009704345.1_ASM970434v1_genomic.fna/checkm_result
[2023-06-17 08:22:09,874] [INFO] Task succeeded: CheckM
[2023-06-17 08:22:09,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:22:09,912] [INFO] ===== Completeness check finished =====
[2023-06-17 08:22:09,912] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:22:09,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009704345.1_ASM970434v1_genomic.fna/markers.fasta)
[2023-06-17 08:22:09,913] [INFO] Task started: Blastn
[2023-06-17 08:22:09,913] [INFO] Running command: blastn -query GCA_009704345.1_ASM970434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg182efeb7-b389-4a43-a111-58989ccf1040/dqc_reference/reference_markers_gtdb.fasta -out GCA_009704345.1_ASM970434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:22:10,554] [INFO] Task succeeded: Blastn
[2023-06-17 08:22:10,560] [INFO] Selected 8 target genomes.
[2023-06-17 08:22:10,560] [INFO] Target genome list was writen to GCA_009704345.1_ASM970434v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:22:10,568] [INFO] Task started: fastANI
[2023-06-17 08:22:10,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg1688ff12-ef59-428c-a7fe-e5f5180a76fc/GCA_009704345.1_ASM970434v1_genomic.fna.gz --refList GCA_009704345.1_ASM970434v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009704345.1_ASM970434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:22:12,687] [INFO] Task succeeded: fastANI
[2023-06-17 08:22:12,694] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:22:12,694] [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_009704345.1	s__AcAMD-5 sp009704345	100.0	303	308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__AcAMD-5	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016870575.1	s__AcAMD-5 sp016870575	78.9862	82	308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__AcAMD-5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:22:12,696] [INFO] GTDB search result was written to GCA_009704345.1_ASM970434v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:22:12,697] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:22:12,699] [INFO] DFAST_QC result json was written to GCA_009704345.1_ASM970434v1_genomic.fna/dqc_result.json
[2023-06-17 08:22:12,700] [INFO] DFAST_QC completed!
[2023-06-17 08:22:12,700] [INFO] Total running time: 0h0m27s