[2024-01-25 20:20:05,644] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg16c313a4-543d-4168-8053-dd1a90e2ba33/dqc_reference
[2024-01-25 20:20:06,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:06,777] [INFO] Task started: Prodigal
[2024-01-25 20:20:06,777] [INFO] Running command: gunzip -c /var/lib/cwl/stg69425e98-d338-45af-8e3b-6f0e55333579/GCF_027594745.1_ASM2759474v1_genomic.fna.gz | prodigal -d GCF_027594745.1_ASM2759474v1_genomic.fna/cds.fna -a GCF_027594745.1_ASM2759474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:24,177] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:24,177] [INFO] Task started: HMMsearch
[2024-01-25 20:20:24,177] [INFO] Running command: hmmsearch --tblout GCF_027594745.1_ASM2759474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16c313a4-543d-4168-8053-dd1a90e2ba33/dqc_reference/reference_markers.hmm GCF_027594745.1_ASM2759474v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:24,412] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:24,413] [INFO] Found 6/6 markers.
[2024-01-25 20:20:24,444] [INFO] Query marker FASTA was written to GCF_027594745.1_ASM2759474v1_genomic.fna/markers.fasta
[2024-01-25 20:20:24,444] [INFO] Task started: Blastn
[2024-01-25 20:20:24,445] [INFO] Running command: blastn -query GCF_027594745.1_ASM2759474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c313a4-543d-4168-8053-dd1a90e2ba33/dqc_reference/reference_markers.fasta -out GCF_027594745.1_ASM2759474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:25,019] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:25,022] [INFO] Selected 28 target genomes.
[2024-01-25 20:20:25,022] [INFO] Target genome list was writen to GCF_027594745.1_ASM2759474v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:25,042] [INFO] Task started: fastANI
[2024-01-25 20:20:25,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg69425e98-d338-45af-8e3b-6f0e55333579/GCF_027594745.1_ASM2759474v1_genomic.fna.gz --refList GCF_027594745.1_ASM2759474v1_genomic.fna/target_genomes.txt --output GCF_027594745.1_ASM2759474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:41,543] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:41,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16c313a4-543d-4168-8053-dd1a90e2ba33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:41,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16c313a4-543d-4168-8053-dd1a90e2ba33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:41,546] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:20:41,546] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-25 20:20:41,546] [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
--------------------------------------------------------------------------------
[2024-01-25 20:20:41,547] [INFO] DFAST Taxonomy check result was written to GCF_027594745.1_ASM2759474v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:41,548] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:41,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:41,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16c313a4-543d-4168-8053-dd1a90e2ba33/dqc_reference/checkm_data
[2024-01-25 20:20:41,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:41,597] [INFO] Task started: CheckM
[2024-01-25 20:20:41,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027594745.1_ASM2759474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027594745.1_ASM2759474v1_genomic.fna/checkm_input GCF_027594745.1_ASM2759474v1_genomic.fna/checkm_result
[2024-01-25 20:21:28,556] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:28,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:28,572] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:28,572] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:28,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027594745.1_ASM2759474v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:28,573] [INFO] Task started: Blastn
[2024-01-25 20:21:28,573] [INFO] Running command: blastn -query GCF_027594745.1_ASM2759474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c313a4-543d-4168-8053-dd1a90e2ba33/dqc_reference/reference_markers_gtdb.fasta -out GCF_027594745.1_ASM2759474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:29,330] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:29,333] [INFO] Selected 22 target genomes.
[2024-01-25 20:21:29,333] [INFO] Target genome list was writen to GCF_027594745.1_ASM2759474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:29,357] [INFO] Task started: fastANI
[2024-01-25 20:21:29,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg69425e98-d338-45af-8e3b-6f0e55333579/GCF_027594745.1_ASM2759474v1_genomic.fna.gz --refList GCF_027594745.1_ASM2759474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027594745.1_ASM2759474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:59,076] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:59,079] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:59,079] [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
GCF_000250635.1	s__Saprospira grandis_B	96.6057	1321	1433	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Saprospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000275825.1	s__Saprospira grandis_A	93.6198	1329	1433	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Saprospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:59,081] [INFO] GTDB search result was written to GCF_027594745.1_ASM2759474v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:59,081] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:59,083] [INFO] DFAST_QC result json was written to GCF_027594745.1_ASM2759474v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:59,083] [INFO] DFAST_QC completed!
[2024-01-25 20:21:59,083] [INFO] Total running time: 0h1m53s