[2023-06-30 12:42:33,265] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:42:33,267] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:42:33,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d8817b7-bc01-4a5a-a925-9f7ea566e6bb/dqc_reference
[2023-06-30 12:42:34,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:42:34,545] [INFO] Task started: Prodigal
[2023-06-30 12:42:34,546] [INFO] Running command: gunzip -c /var/lib/cwl/stgac12f9ff-9e97-47f2-a7af-7b164129c1c9/GCA_016708265.1_ASM1670826v1_genomic.fna.gz | prodigal -d GCA_016708265.1_ASM1670826v1_genomic.fna/cds.fna -a GCA_016708265.1_ASM1670826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:42:50,771] [INFO] Task succeeded: Prodigal
[2023-06-30 12:42:50,771] [INFO] Task started: HMMsearch
[2023-06-30 12:42:50,771] [INFO] Running command: hmmsearch --tblout GCA_016708265.1_ASM1670826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d8817b7-bc01-4a5a-a925-9f7ea566e6bb/dqc_reference/reference_markers.hmm GCA_016708265.1_ASM1670826v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:42:51,049] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:42:51,051] [INFO] Found 6/6 markers.
[2023-06-30 12:42:51,092] [INFO] Query marker FASTA was written to GCA_016708265.1_ASM1670826v1_genomic.fna/markers.fasta
[2023-06-30 12:42:51,093] [INFO] Task started: Blastn
[2023-06-30 12:42:51,093] [INFO] Running command: blastn -query GCA_016708265.1_ASM1670826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d8817b7-bc01-4a5a-a925-9f7ea566e6bb/dqc_reference/reference_markers.fasta -out GCA_016708265.1_ASM1670826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:42:51,678] [INFO] Task succeeded: Blastn
[2023-06-30 12:42:51,683] [INFO] Selected 29 target genomes.
[2023-06-30 12:42:51,684] [INFO] Target genome list was writen to GCA_016708265.1_ASM1670826v1_genomic.fna/target_genomes.txt
[2023-06-30 12:42:51,691] [INFO] Task started: fastANI
[2023-06-30 12:42:51,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgac12f9ff-9e97-47f2-a7af-7b164129c1c9/GCA_016708265.1_ASM1670826v1_genomic.fna.gz --refList GCA_016708265.1_ASM1670826v1_genomic.fna/target_genomes.txt --output GCA_016708265.1_ASM1670826v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:43:09,346] [INFO] Task succeeded: fastANI
[2023-06-30 12:43:09,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d8817b7-bc01-4a5a-a925-9f7ea566e6bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:43:09,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d8817b7-bc01-4a5a-a925-9f7ea566e6bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:43:09,349] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:43:09,349] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 12:43:09,350] [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 12:43:09,352] [INFO] DFAST Taxonomy check result was written to GCA_016708265.1_ASM1670826v1_genomic.fna/tc_result.tsv
[2023-06-30 12:43:09,353] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:43:09,353] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:43:09,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d8817b7-bc01-4a5a-a925-9f7ea566e6bb/dqc_reference/checkm_data
[2023-06-30 12:43:09,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:43:09,403] [INFO] Task started: CheckM
[2023-06-30 12:43:09,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708265.1_ASM1670826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708265.1_ASM1670826v1_genomic.fna/checkm_input GCA_016708265.1_ASM1670826v1_genomic.fna/checkm_result
[2023-06-30 12:44:00,119] [INFO] Task succeeded: CheckM
[2023-06-30 12:44:00,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 12:44:00,146] [INFO] ===== Completeness check finished =====
[2023-06-30 12:44:00,146] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:44:00,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708265.1_ASM1670826v1_genomic.fna/markers.fasta)
[2023-06-30 12:44:00,147] [INFO] Task started: Blastn
[2023-06-30 12:44:00,147] [INFO] Running command: blastn -query GCA_016708265.1_ASM1670826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d8817b7-bc01-4a5a-a925-9f7ea566e6bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708265.1_ASM1670826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:44:00,865] [INFO] Task succeeded: Blastn
[2023-06-30 12:44:00,871] [INFO] Selected 29 target genomes.
[2023-06-30 12:44:00,871] [INFO] Target genome list was writen to GCA_016708265.1_ASM1670826v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:44:00,920] [INFO] Task started: fastANI
[2023-06-30 12:44:00,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgac12f9ff-9e97-47f2-a7af-7b164129c1c9/GCA_016708265.1_ASM1670826v1_genomic.fna.gz --refList GCA_016708265.1_ASM1670826v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708265.1_ASM1670826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:44:18,961] [INFO] Task succeeded: fastANI
[2023-06-30 12:44:18,967] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:44:18,967] [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_016708265.1	s__JADJGA01 sp016708265	100.0	1460	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJGA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016714445.1	s__OLB9 sp016714445	75.8614	57	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	97.58	97.50	0.85	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-30 12:44:18,969] [INFO] GTDB search result was written to GCA_016708265.1_ASM1670826v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:44:18,969] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:44:18,972] [INFO] DFAST_QC result json was written to GCA_016708265.1_ASM1670826v1_genomic.fna/dqc_result.json
[2023-06-30 12:44:18,972] [INFO] DFAST_QC completed!
[2023-06-30 12:44:18,972] [INFO] Total running time: 0h1m46s