[2023-06-28 12:14:24,526] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:14:24,530] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:14:24,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b23338a-bed3-4348-a294-0863c08f3acf/dqc_reference
[2023-06-28 12:14:25,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:14:25,907] [INFO] Task started: Prodigal
[2023-06-28 12:14:25,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c91557e-33a2-48fe-aab5-265764b0c983/GCA_015656635.1_ASM1565663v1_genomic.fna.gz | prodigal -d GCA_015656635.1_ASM1565663v1_genomic.fna/cds.fna -a GCA_015656635.1_ASM1565663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:14:29,712] [INFO] Task succeeded: Prodigal
[2023-06-28 12:14:29,712] [INFO] Task started: HMMsearch
[2023-06-28 12:14:29,712] [INFO] Running command: hmmsearch --tblout GCA_015656635.1_ASM1565663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b23338a-bed3-4348-a294-0863c08f3acf/dqc_reference/reference_markers.hmm GCA_015656635.1_ASM1565663v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:14:29,988] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:14:29,989] [INFO] Found 6/6 markers.
[2023-06-28 12:14:30,010] [INFO] Query marker FASTA was written to GCA_015656635.1_ASM1565663v1_genomic.fna/markers.fasta
[2023-06-28 12:14:30,010] [INFO] Task started: Blastn
[2023-06-28 12:14:30,011] [INFO] Running command: blastn -query GCA_015656635.1_ASM1565663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b23338a-bed3-4348-a294-0863c08f3acf/dqc_reference/reference_markers.fasta -out GCA_015656635.1_ASM1565663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:14:30,657] [INFO] Task succeeded: Blastn
[2023-06-28 12:14:30,661] [INFO] Selected 20 target genomes.
[2023-06-28 12:14:30,661] [INFO] Target genome list was writen to GCA_015656635.1_ASM1565663v1_genomic.fna/target_genomes.txt
[2023-06-28 12:14:30,670] [INFO] Task started: fastANI
[2023-06-28 12:14:30,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c91557e-33a2-48fe-aab5-265764b0c983/GCA_015656635.1_ASM1565663v1_genomic.fna.gz --refList GCA_015656635.1_ASM1565663v1_genomic.fna/target_genomes.txt --output GCA_015656635.1_ASM1565663v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:14:41,107] [INFO] Task succeeded: fastANI
[2023-06-28 12:14:41,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b23338a-bed3-4348-a294-0863c08f3acf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:14:41,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b23338a-bed3-4348-a294-0863c08f3acf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:14:41,110] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:14:41,110] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:14:41,110] [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
--------------------------------------------------------------------------------
[2023-06-28 12:14:41,112] [INFO] DFAST Taxonomy check result was written to GCA_015656635.1_ASM1565663v1_genomic.fna/tc_result.tsv
[2023-06-28 12:14:41,113] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:14:41,113] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:14:41,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b23338a-bed3-4348-a294-0863c08f3acf/dqc_reference/checkm_data
[2023-06-28 12:14:41,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:14:41,141] [INFO] Task started: CheckM
[2023-06-28 12:14:41,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015656635.1_ASM1565663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015656635.1_ASM1565663v1_genomic.fna/checkm_input GCA_015656635.1_ASM1565663v1_genomic.fna/checkm_result
[2023-06-28 12:15:00,575] [INFO] Task succeeded: CheckM
[2023-06-28 12:15:00,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:15:00,596] [INFO] ===== Completeness check finished =====
[2023-06-28 12:15:00,597] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:15:00,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015656635.1_ASM1565663v1_genomic.fna/markers.fasta)
[2023-06-28 12:15:00,597] [INFO] Task started: Blastn
[2023-06-28 12:15:00,598] [INFO] Running command: blastn -query GCA_015656635.1_ASM1565663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b23338a-bed3-4348-a294-0863c08f3acf/dqc_reference/reference_markers_gtdb.fasta -out GCA_015656635.1_ASM1565663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:15:01,615] [INFO] Task succeeded: Blastn
[2023-06-28 12:15:01,619] [INFO] Selected 22 target genomes.
[2023-06-28 12:15:01,619] [INFO] Target genome list was writen to GCA_015656635.1_ASM1565663v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:15:01,633] [INFO] Task started: fastANI
[2023-06-28 12:15:01,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c91557e-33a2-48fe-aab5-265764b0c983/GCA_015656635.1_ASM1565663v1_genomic.fna.gz --refList GCA_015656635.1_ASM1565663v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015656635.1_ASM1565663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:15:12,490] [INFO] Task succeeded: fastANI
[2023-06-28 12:15:12,495] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:15:12,495] [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_017631885.1	s__UBA1765 sp017631885	99.4039	579	593	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__UBA1765	95.0	98.68	97.24	0.95	0.90	4	conclusive
GCA_017625775.1	s__UBA1765 sp017625775	83.1383	281	593	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__UBA1765	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001462345.1	s__Fibro-01 sp001462345	76.7995	77	593	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibro-01	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012515825.1	s__Fibro-01 sp012515825	76.337	52	593	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibro-01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:15:12,497] [INFO] GTDB search result was written to GCA_015656635.1_ASM1565663v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:15:12,498] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:15:12,500] [INFO] DFAST_QC result json was written to GCA_015656635.1_ASM1565663v1_genomic.fna/dqc_result.json
[2023-06-28 12:15:12,500] [INFO] DFAST_QC completed!
[2023-06-28 12:15:12,501] [INFO] Total running time: 0h0m48s