[2023-06-30 16:59:53,839] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:59:53,842] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:59:53,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e33b377-4fe6-4049-a5a1-ecbd9b9d771a/dqc_reference
[2023-06-30 16:59:56,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:59:56,358] [INFO] Task started: Prodigal
[2023-06-30 16:59:56,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg8eb24848-a0f4-4936-b99c-a93a7e94e8a2/GCA_016764875.1_ASM1676487v1_genomic.fna.gz | prodigal -d GCA_016764875.1_ASM1676487v1_genomic.fna/cds.fna -a GCA_016764875.1_ASM1676487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:00:02,840] [INFO] Task succeeded: Prodigal
[2023-06-30 17:00:02,840] [INFO] Task started: HMMsearch
[2023-06-30 17:00:02,841] [INFO] Running command: hmmsearch --tblout GCA_016764875.1_ASM1676487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e33b377-4fe6-4049-a5a1-ecbd9b9d771a/dqc_reference/reference_markers.hmm GCA_016764875.1_ASM1676487v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:00:03,133] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:00:03,135] [INFO] Found 6/6 markers.
[2023-06-30 17:00:03,165] [INFO] Query marker FASTA was written to GCA_016764875.1_ASM1676487v1_genomic.fna/markers.fasta
[2023-06-30 17:00:03,166] [INFO] Task started: Blastn
[2023-06-30 17:00:03,166] [INFO] Running command: blastn -query GCA_016764875.1_ASM1676487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e33b377-4fe6-4049-a5a1-ecbd9b9d771a/dqc_reference/reference_markers.fasta -out GCA_016764875.1_ASM1676487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:03,849] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:03,855] [INFO] Selected 29 target genomes.
[2023-06-30 17:00:03,855] [INFO] Target genome list was writen to GCA_016764875.1_ASM1676487v1_genomic.fna/target_genomes.txt
[2023-06-30 17:00:03,868] [INFO] Task started: fastANI
[2023-06-30 17:00:03,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eb24848-a0f4-4936-b99c-a93a7e94e8a2/GCA_016764875.1_ASM1676487v1_genomic.fna.gz --refList GCA_016764875.1_ASM1676487v1_genomic.fna/target_genomes.txt --output GCA_016764875.1_ASM1676487v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:00:23,717] [INFO] Task succeeded: fastANI
[2023-06-30 17:00:23,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e33b377-4fe6-4049-a5a1-ecbd9b9d771a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:00:23,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e33b377-4fe6-4049-a5a1-ecbd9b9d771a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:00:23,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:00:23,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 17:00:23,721] [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
--------------------------------------------------------------------------------
[2023-06-30 17:00:23,725] [INFO] DFAST Taxonomy check result was written to GCA_016764875.1_ASM1676487v1_genomic.fna/tc_result.tsv
[2023-06-30 17:00:23,726] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:00:23,726] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:00:23,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e33b377-4fe6-4049-a5a1-ecbd9b9d771a/dqc_reference/checkm_data
[2023-06-30 17:00:23,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:00:23,762] [INFO] Task started: CheckM
[2023-06-30 17:00:23,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016764875.1_ASM1676487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016764875.1_ASM1676487v1_genomic.fna/checkm_input GCA_016764875.1_ASM1676487v1_genomic.fna/checkm_result
[2023-06-30 17:00:49,439] [INFO] Task succeeded: CheckM
[2023-06-30 17:00:49,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:00:49,466] [INFO] ===== Completeness check finished =====
[2023-06-30 17:00:49,467] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:00:49,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016764875.1_ASM1676487v1_genomic.fna/markers.fasta)
[2023-06-30 17:00:49,467] [INFO] Task started: Blastn
[2023-06-30 17:00:49,468] [INFO] Running command: blastn -query GCA_016764875.1_ASM1676487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e33b377-4fe6-4049-a5a1-ecbd9b9d771a/dqc_reference/reference_markers_gtdb.fasta -out GCA_016764875.1_ASM1676487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:50,519] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:50,524] [INFO] Selected 24 target genomes.
[2023-06-30 17:00:50,524] [INFO] Target genome list was writen to GCA_016764875.1_ASM1676487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:00:50,543] [INFO] Task started: fastANI
[2023-06-30 17:00:50,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eb24848-a0f4-4936-b99c-a93a7e94e8a2/GCA_016764875.1_ASM1676487v1_genomic.fna.gz --refList GCA_016764875.1_ASM1676487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016764875.1_ASM1676487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:01:04,301] [INFO] Task succeeded: fastANI
[2023-06-30 17:01:04,306] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:01:04,306] [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_016764875.1	s__NORP240 sp016764875	100.0	800	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__NORP240	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-30 17:01:04,324] [INFO] GTDB search result was written to GCA_016764875.1_ASM1676487v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:01:04,325] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:01:04,329] [INFO] DFAST_QC result json was written to GCA_016764875.1_ASM1676487v1_genomic.fna/dqc_result.json
[2023-06-30 17:01:04,330] [INFO] DFAST_QC completed!
[2023-06-30 17:01:04,330] [INFO] Total running time: 0h1m10s