[2023-06-29 12:58:17,200] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:58:17,202] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:58:17,202] [INFO] DQC Reference Directory: /var/lib/cwl/stgad22d614-8ea2-4f0c-848c-9417384f29c2/dqc_reference
[2023-06-29 12:58:19,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:58:19,580] [INFO] Task started: Prodigal
[2023-06-29 12:58:19,580] [INFO] Running command: gunzip -c /var/lib/cwl/stg32fdcc61-7ff9-4c52-9d57-d842a750683f/GCA_020624445.1_ASM2062444v1_genomic.fna.gz | prodigal -d GCA_020624445.1_ASM2062444v1_genomic.fna/cds.fna -a GCA_020624445.1_ASM2062444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:58:30,090] [INFO] Task succeeded: Prodigal
[2023-06-29 12:58:30,091] [INFO] Task started: HMMsearch
[2023-06-29 12:58:30,091] [INFO] Running command: hmmsearch --tblout GCA_020624445.1_ASM2062444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad22d614-8ea2-4f0c-848c-9417384f29c2/dqc_reference/reference_markers.hmm GCA_020624445.1_ASM2062444v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:58:30,266] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:58:30,268] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg32fdcc61-7ff9-4c52-9d57-d842a750683f/GCA_020624445.1_ASM2062444v1_genomic.fna.gz]
[2023-06-29 12:58:30,295] [INFO] Query marker FASTA was written to GCA_020624445.1_ASM2062444v1_genomic.fna/markers.fasta
[2023-06-29 12:58:30,295] [INFO] Task started: Blastn
[2023-06-29 12:58:30,295] [INFO] Running command: blastn -query GCA_020624445.1_ASM2062444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad22d614-8ea2-4f0c-848c-9417384f29c2/dqc_reference/reference_markers.fasta -out GCA_020624445.1_ASM2062444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:58:30,780] [INFO] Task succeeded: Blastn
[2023-06-29 12:58:30,784] [INFO] Selected 22 target genomes.
[2023-06-29 12:58:30,784] [INFO] Target genome list was writen to GCA_020624445.1_ASM2062444v1_genomic.fna/target_genomes.txt
[2023-06-29 12:58:30,787] [INFO] Task started: fastANI
[2023-06-29 12:58:30,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg32fdcc61-7ff9-4c52-9d57-d842a750683f/GCA_020624445.1_ASM2062444v1_genomic.fna.gz --refList GCA_020624445.1_ASM2062444v1_genomic.fna/target_genomes.txt --output GCA_020624445.1_ASM2062444v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:58:40,343] [INFO] Task succeeded: fastANI
[2023-06-29 12:58:40,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad22d614-8ea2-4f0c-848c-9417384f29c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:58:40,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad22d614-8ea2-4f0c-848c-9417384f29c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:58:40,346] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:58:40,346] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:58:40,346] [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
--------------------------------------------------------------------------------
[2023-06-29 12:58:40,348] [INFO] DFAST Taxonomy check result was written to GCA_020624445.1_ASM2062444v1_genomic.fna/tc_result.tsv
[2023-06-29 12:58:40,348] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:58:40,348] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:58:40,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad22d614-8ea2-4f0c-848c-9417384f29c2/dqc_reference/checkm_data
[2023-06-29 12:58:40,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:58:40,379] [INFO] Task started: CheckM
[2023-06-29 12:58:40,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020624445.1_ASM2062444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020624445.1_ASM2062444v1_genomic.fna/checkm_input GCA_020624445.1_ASM2062444v1_genomic.fna/checkm_result
[2023-06-29 12:59:15,056] [INFO] Task succeeded: CheckM
[2023-06-29 12:59:15,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.71%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 12:59:15,075] [INFO] ===== Completeness check finished =====
[2023-06-29 12:59:15,075] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:59:15,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020624445.1_ASM2062444v1_genomic.fna/markers.fasta)
[2023-06-29 12:59:15,076] [INFO] Task started: Blastn
[2023-06-29 12:59:15,076] [INFO] Running command: blastn -query GCA_020624445.1_ASM2062444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad22d614-8ea2-4f0c-848c-9417384f29c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_020624445.1_ASM2062444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:59:15,527] [INFO] Task succeeded: Blastn
[2023-06-29 12:59:15,531] [INFO] Selected 22 target genomes.
[2023-06-29 12:59:15,531] [INFO] Target genome list was writen to GCA_020624445.1_ASM2062444v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:59:15,546] [INFO] Task started: fastANI
[2023-06-29 12:59:15,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg32fdcc61-7ff9-4c52-9d57-d842a750683f/GCA_020624445.1_ASM2062444v1_genomic.fna.gz --refList GCA_020624445.1_ASM2062444v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020624445.1_ASM2062444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:59:26,286] [INFO] Task succeeded: fastANI
[2023-06-29 12:59:26,290] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:59:26,290] [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_902784755.1	s__Prevotella sp902784755	98.8976	54	64	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.59	97.59	0.83	0.83	2	conclusive
--------------------------------------------------------------------------------
[2023-06-29 12:59:26,292] [INFO] GTDB search result was written to GCA_020624445.1_ASM2062444v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:59:26,293] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:59:26,295] [INFO] DFAST_QC result json was written to GCA_020624445.1_ASM2062444v1_genomic.fna/dqc_result.json
[2023-06-29 12:59:26,295] [INFO] DFAST_QC completed!
[2023-06-29 12:59:26,295] [INFO] Total running time: 0h1m9s