[2023-06-17 16:13:26,731] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:13:26,745] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:13:26,745] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbd4ff67-e23e-4005-8943-30a1e37a0b12/dqc_reference
[2023-06-17 16:13:28,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:13:28,083] [INFO] Task started: Prodigal
[2023-06-17 16:13:28,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ff7e5ae-181b-46e3-8b5d-20ed848adb3b/GCA_003022985.1_ASM302298v1_genomic.fna.gz | prodigal -d GCA_003022985.1_ASM302298v1_genomic.fna/cds.fna -a GCA_003022985.1_ASM302298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:13:37,100] [INFO] Task succeeded: Prodigal
[2023-06-17 16:13:37,101] [INFO] Task started: HMMsearch
[2023-06-17 16:13:37,101] [INFO] Running command: hmmsearch --tblout GCA_003022985.1_ASM302298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbd4ff67-e23e-4005-8943-30a1e37a0b12/dqc_reference/reference_markers.hmm GCA_003022985.1_ASM302298v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:13:37,321] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:13:37,323] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1ff7e5ae-181b-46e3-8b5d-20ed848adb3b/GCA_003022985.1_ASM302298v1_genomic.fna.gz]
[2023-06-17 16:13:37,358] [INFO] Query marker FASTA was written to GCA_003022985.1_ASM302298v1_genomic.fna/markers.fasta
[2023-06-17 16:13:37,359] [INFO] Task started: Blastn
[2023-06-17 16:13:37,359] [INFO] Running command: blastn -query GCA_003022985.1_ASM302298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd4ff67-e23e-4005-8943-30a1e37a0b12/dqc_reference/reference_markers.fasta -out GCA_003022985.1_ASM302298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:13:37,981] [INFO] Task succeeded: Blastn
[2023-06-17 16:13:37,985] [INFO] Selected 14 target genomes.
[2023-06-17 16:13:37,985] [INFO] Target genome list was writen to GCA_003022985.1_ASM302298v1_genomic.fna/target_genomes.txt
[2023-06-17 16:13:37,989] [INFO] Task started: fastANI
[2023-06-17 16:13:37,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ff7e5ae-181b-46e3-8b5d-20ed848adb3b/GCA_003022985.1_ASM302298v1_genomic.fna.gz --refList GCA_003022985.1_ASM302298v1_genomic.fna/target_genomes.txt --output GCA_003022985.1_ASM302298v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:13:50,871] [INFO] Task succeeded: fastANI
[2023-06-17 16:13:50,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbd4ff67-e23e-4005-8943-30a1e37a0b12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:13:50,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbd4ff67-e23e-4005-8943-30a1e37a0b12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:13:50,874] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:13:50,874] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 16:13:50,874] [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 16:13:50,877] [INFO] DFAST Taxonomy check result was written to GCA_003022985.1_ASM302298v1_genomic.fna/tc_result.tsv
[2023-06-17 16:13:50,877] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:13:50,878] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:13:50,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbd4ff67-e23e-4005-8943-30a1e37a0b12/dqc_reference/checkm_data
[2023-06-17 16:13:50,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:13:50,913] [INFO] Task started: CheckM
[2023-06-17 16:13:50,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003022985.1_ASM302298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003022985.1_ASM302298v1_genomic.fna/checkm_input GCA_003022985.1_ASM302298v1_genomic.fna/checkm_result
[2023-06-17 16:14:22,870] [INFO] Task succeeded: CheckM
[2023-06-17 16:14:22,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:14:22,892] [INFO] ===== Completeness check finished =====
[2023-06-17 16:14:22,893] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:14:22,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003022985.1_ASM302298v1_genomic.fna/markers.fasta)
[2023-06-17 16:14:22,893] [INFO] Task started: Blastn
[2023-06-17 16:14:22,894] [INFO] Running command: blastn -query GCA_003022985.1_ASM302298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd4ff67-e23e-4005-8943-30a1e37a0b12/dqc_reference/reference_markers_gtdb.fasta -out GCA_003022985.1_ASM302298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:14:23,756] [INFO] Task succeeded: Blastn
[2023-06-17 16:14:23,761] [INFO] Selected 18 target genomes.
[2023-06-17 16:14:23,761] [INFO] Target genome list was writen to GCA_003022985.1_ASM302298v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:14:23,777] [INFO] Task started: fastANI
[2023-06-17 16:14:23,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ff7e5ae-181b-46e3-8b5d-20ed848adb3b/GCA_003022985.1_ASM302298v1_genomic.fna.gz --refList GCA_003022985.1_ASM302298v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003022985.1_ASM302298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:14:35,384] [INFO] Task succeeded: fastANI
[2023-06-17 16:14:35,389] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:14:35,390] [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_003022985.1	s__SW-11-45-7 sp003022985	100.0	523	531	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__SW-11-45-7;g__SW-11-45-7	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-17 16:14:35,392] [INFO] GTDB search result was written to GCA_003022985.1_ASM302298v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:14:35,393] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:14:35,395] [INFO] DFAST_QC result json was written to GCA_003022985.1_ASM302298v1_genomic.fna/dqc_result.json
[2023-06-17 16:14:35,396] [INFO] DFAST_QC completed!
[2023-06-17 16:14:35,396] [INFO] Total running time: 0h1m9s