[2023-06-29 03:05:49,803] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:05:49,820] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:05:49,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b034950-0566-4f6c-9a9c-7c2eeeb95caa/dqc_reference
[2023-06-29 03:05:51,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:05:51,166] [INFO] Task started: Prodigal
[2023-06-29 03:05:51,167] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc7f0c9b-e40f-48ea-9f69-fcfd8e6fa855/GCA_020718385.1_ASM2071838v1_genomic.fna.gz | prodigal -d GCA_020718385.1_ASM2071838v1_genomic.fna/cds.fna -a GCA_020718385.1_ASM2071838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:05:58,674] [INFO] Task succeeded: Prodigal
[2023-06-29 03:05:58,674] [INFO] Task started: HMMsearch
[2023-06-29 03:05:58,674] [INFO] Running command: hmmsearch --tblout GCA_020718385.1_ASM2071838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b034950-0566-4f6c-9a9c-7c2eeeb95caa/dqc_reference/reference_markers.hmm GCA_020718385.1_ASM2071838v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:05:58,975] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:05:58,976] [INFO] Found 6/6 markers.
[2023-06-29 03:05:59,001] [INFO] Query marker FASTA was written to GCA_020718385.1_ASM2071838v1_genomic.fna/markers.fasta
[2023-06-29 03:05:59,002] [INFO] Task started: Blastn
[2023-06-29 03:05:59,002] [INFO] Running command: blastn -query GCA_020718385.1_ASM2071838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b034950-0566-4f6c-9a9c-7c2eeeb95caa/dqc_reference/reference_markers.fasta -out GCA_020718385.1_ASM2071838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:05:59,625] [INFO] Task succeeded: Blastn
[2023-06-29 03:05:59,630] [INFO] Selected 34 target genomes.
[2023-06-29 03:05:59,631] [INFO] Target genome list was writen to GCA_020718385.1_ASM2071838v1_genomic.fna/target_genomes.txt
[2023-06-29 03:05:59,635] [INFO] Task started: fastANI
[2023-06-29 03:05:59,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc7f0c9b-e40f-48ea-9f69-fcfd8e6fa855/GCA_020718385.1_ASM2071838v1_genomic.fna.gz --refList GCA_020718385.1_ASM2071838v1_genomic.fna/target_genomes.txt --output GCA_020718385.1_ASM2071838v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:06:20,067] [INFO] Task succeeded: fastANI
[2023-06-29 03:06:20,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b034950-0566-4f6c-9a9c-7c2eeeb95caa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:06:20,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b034950-0566-4f6c-9a9c-7c2eeeb95caa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:06:20,070] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:06:20,070] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 03:06:20,070] [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 03:06:20,078] [INFO] DFAST Taxonomy check result was written to GCA_020718385.1_ASM2071838v1_genomic.fna/tc_result.tsv
[2023-06-29 03:06:20,079] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:06:20,079] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:06:20,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b034950-0566-4f6c-9a9c-7c2eeeb95caa/dqc_reference/checkm_data
[2023-06-29 03:06:20,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:06:20,121] [INFO] Task started: CheckM
[2023-06-29 03:06:20,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020718385.1_ASM2071838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020718385.1_ASM2071838v1_genomic.fna/checkm_input GCA_020718385.1_ASM2071838v1_genomic.fna/checkm_result
[2023-06-29 03:06:47,864] [INFO] Task succeeded: CheckM
[2023-06-29 03:06:47,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 03:06:47,889] [INFO] ===== Completeness check finished =====
[2023-06-29 03:06:47,889] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:06:47,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020718385.1_ASM2071838v1_genomic.fna/markers.fasta)
[2023-06-29 03:06:47,890] [INFO] Task started: Blastn
[2023-06-29 03:06:47,890] [INFO] Running command: blastn -query GCA_020718385.1_ASM2071838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b034950-0566-4f6c-9a9c-7c2eeeb95caa/dqc_reference/reference_markers_gtdb.fasta -out GCA_020718385.1_ASM2071838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:06:48,682] [INFO] Task succeeded: Blastn
[2023-06-29 03:06:48,688] [INFO] Selected 37 target genomes.
[2023-06-29 03:06:48,688] [INFO] Target genome list was writen to GCA_020718385.1_ASM2071838v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:06:48,722] [INFO] Task started: fastANI
[2023-06-29 03:06:48,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc7f0c9b-e40f-48ea-9f69-fcfd8e6fa855/GCA_020718385.1_ASM2071838v1_genomic.fna.gz --refList GCA_020718385.1_ASM2071838v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020718385.1_ASM2071838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:07:06,424] [INFO] Task succeeded: fastANI
[2023-06-29 03:07:06,431] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:07:06,432] [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_013153575.1	s__JAADGE01 sp013153575	76.3768	98	746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JAADGE01;g__JAADGE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152535.1	s__JAADGE01 sp013152535	76.2724	176	746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JAADGE01;g__JAADGE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153865.1	s__JAADGE01 sp013153865	75.947	93	746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JAADGE01;g__JAADGE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:07:06,434] [INFO] GTDB search result was written to GCA_020718385.1_ASM2071838v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:07:06,434] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:07:06,437] [INFO] DFAST_QC result json was written to GCA_020718385.1_ASM2071838v1_genomic.fna/dqc_result.json
[2023-06-29 03:07:06,437] [INFO] DFAST_QC completed!
[2023-06-29 03:07:06,437] [INFO] Total running time: 0h1m17s