[2023-06-29 20:13:39,988] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:13:39,998] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:13:39,998] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf3ffe3b-5431-4fa5-80c4-62273cfa6a16/dqc_reference
[2023-06-29 20:13:41,504] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:13:41,505] [INFO] Task started: Prodigal
[2023-06-29 20:13:41,505] [INFO] Running command: gunzip -c /var/lib/cwl/stg813d9557-a844-418d-a622-0a60bc97f44c/GCA_910579765.1_MGBC114937_genomic.fna.gz | prodigal -d GCA_910579765.1_MGBC114937_genomic.fna/cds.fna -a GCA_910579765.1_MGBC114937_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:13:42,622] [INFO] Task succeeded: Prodigal
[2023-06-29 20:13:42,623] [INFO] Task started: HMMsearch
[2023-06-29 20:13:42,623] [INFO] Running command: hmmsearch --tblout GCA_910579765.1_MGBC114937_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf3ffe3b-5431-4fa5-80c4-62273cfa6a16/dqc_reference/reference_markers.hmm GCA_910579765.1_MGBC114937_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:13:42,868] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:13:42,870] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg813d9557-a844-418d-a622-0a60bc97f44c/GCA_910579765.1_MGBC114937_genomic.fna.gz]
[2023-06-29 20:13:42,881] [INFO] Query marker FASTA was written to GCA_910579765.1_MGBC114937_genomic.fna/markers.fasta
[2023-06-29 20:13:42,881] [INFO] Task started: Blastn
[2023-06-29 20:13:42,882] [INFO] Running command: blastn -query GCA_910579765.1_MGBC114937_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf3ffe3b-5431-4fa5-80c4-62273cfa6a16/dqc_reference/reference_markers.fasta -out GCA_910579765.1_MGBC114937_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:13:43,568] [INFO] Task succeeded: Blastn
[2023-06-29 20:13:43,575] [INFO] Selected 19 target genomes.
[2023-06-29 20:13:43,575] [INFO] Target genome list was writen to GCA_910579765.1_MGBC114937_genomic.fna/target_genomes.txt
[2023-06-29 20:13:43,578] [INFO] Task started: fastANI
[2023-06-29 20:13:43,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg813d9557-a844-418d-a622-0a60bc97f44c/GCA_910579765.1_MGBC114937_genomic.fna.gz --refList GCA_910579765.1_MGBC114937_genomic.fna/target_genomes.txt --output GCA_910579765.1_MGBC114937_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:13:48,739] [INFO] Task succeeded: fastANI
[2023-06-29 20:13:48,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf3ffe3b-5431-4fa5-80c4-62273cfa6a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:13:48,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf3ffe3b-5431-4fa5-80c4-62273cfa6a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:13:48,741] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:13:48,741] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:13:48,741] [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 20:13:48,743] [INFO] DFAST Taxonomy check result was written to GCA_910579765.1_MGBC114937_genomic.fna/tc_result.tsv
[2023-06-29 20:13:48,744] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:13:48,744] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:13:48,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf3ffe3b-5431-4fa5-80c4-62273cfa6a16/dqc_reference/checkm_data
[2023-06-29 20:13:48,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:13:48,762] [INFO] Task started: CheckM
[2023-06-29 20:13:48,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910579765.1_MGBC114937_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910579765.1_MGBC114937_genomic.fna/checkm_input GCA_910579765.1_MGBC114937_genomic.fna/checkm_result
[2023-06-29 20:14:01,700] [INFO] Task succeeded: CheckM
[2023-06-29 20:14:01,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:14:01,724] [INFO] ===== Completeness check finished =====
[2023-06-29 20:14:01,724] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:14:01,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910579765.1_MGBC114937_genomic.fna/markers.fasta)
[2023-06-29 20:14:01,724] [INFO] Task started: Blastn
[2023-06-29 20:14:01,725] [INFO] Running command: blastn -query GCA_910579765.1_MGBC114937_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf3ffe3b-5431-4fa5-80c4-62273cfa6a16/dqc_reference/reference_markers_gtdb.fasta -out GCA_910579765.1_MGBC114937_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:02,745] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:02,750] [INFO] Selected 21 target genomes.
[2023-06-29 20:14:02,750] [INFO] Target genome list was writen to GCA_910579765.1_MGBC114937_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:14:02,762] [INFO] Task started: fastANI
[2023-06-29 20:14:02,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg813d9557-a844-418d-a622-0a60bc97f44c/GCA_910579765.1_MGBC114937_genomic.fna.gz --refList GCA_910579765.1_MGBC114937_genomic.fna/target_genomes_gtdb.txt --output GCA_910579765.1_MGBC114937_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:14:09,439] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:09,448] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:14:09,448] [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_002298905.1	s__UBA710 sp002298905	98.1002	180	228	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__UBA710	95.0	98.19	98.19	0.92	0.92	2	conclusive
GCA_014803855.1	s__UBA710 sp014803855	79.3221	116	228	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__UBA710	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017511585.1	s__UBA710 sp017511585	78.2454	73	228	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__UBA710	95.0	97.40	97.40	0.70	0.70	2	-
--------------------------------------------------------------------------------
[2023-06-29 20:14:09,451] [INFO] GTDB search result was written to GCA_910579765.1_MGBC114937_genomic.fna/result_gtdb.tsv
[2023-06-29 20:14:09,452] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:14:09,467] [INFO] DFAST_QC result json was written to GCA_910579765.1_MGBC114937_genomic.fna/dqc_result.json
[2023-06-29 20:14:09,467] [INFO] DFAST_QC completed!
[2023-06-29 20:14:09,468] [INFO] Total running time: 0h0m29s