[2023-06-19 08:51:16,673] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:51:16,676] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:51:16,676] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb05d68b-dd64-4ba8-8cdf-662610865d41/dqc_reference
[2023-06-19 08:51:17,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:51:17,933] [INFO] Task started: Prodigal
[2023-06-19 08:51:17,933] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2a61107-113b-4955-8094-594b5d8b6f9b/GCA_018004645.1_ASM1800464v1_genomic.fna.gz | prodigal -d GCA_018004645.1_ASM1800464v1_genomic.fna/cds.fna -a GCA_018004645.1_ASM1800464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:51:33,407] [INFO] Task succeeded: Prodigal
[2023-06-19 08:51:33,407] [INFO] Task started: HMMsearch
[2023-06-19 08:51:33,407] [INFO] Running command: hmmsearch --tblout GCA_018004645.1_ASM1800464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb05d68b-dd64-4ba8-8cdf-662610865d41/dqc_reference/reference_markers.hmm GCA_018004645.1_ASM1800464v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:51:33,692] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:51:33,694] [INFO] Found 6/6 markers.
[2023-06-19 08:51:33,732] [INFO] Query marker FASTA was written to GCA_018004645.1_ASM1800464v1_genomic.fna/markers.fasta
[2023-06-19 08:51:33,733] [INFO] Task started: Blastn
[2023-06-19 08:51:33,733] [INFO] Running command: blastn -query GCA_018004645.1_ASM1800464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb05d68b-dd64-4ba8-8cdf-662610865d41/dqc_reference/reference_markers.fasta -out GCA_018004645.1_ASM1800464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:51:34,331] [INFO] Task succeeded: Blastn
[2023-06-19 08:51:34,336] [INFO] Selected 22 target genomes.
[2023-06-19 08:51:34,337] [INFO] Target genome list was writen to GCA_018004645.1_ASM1800464v1_genomic.fna/target_genomes.txt
[2023-06-19 08:51:34,344] [INFO] Task started: fastANI
[2023-06-19 08:51:34,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a61107-113b-4955-8094-594b5d8b6f9b/GCA_018004645.1_ASM1800464v1_genomic.fna.gz --refList GCA_018004645.1_ASM1800464v1_genomic.fna/target_genomes.txt --output GCA_018004645.1_ASM1800464v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:51:49,527] [INFO] Task succeeded: fastANI
[2023-06-19 08:51:49,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb05d68b-dd64-4ba8-8cdf-662610865d41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:51:49,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb05d68b-dd64-4ba8-8cdf-662610865d41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:51:49,531] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:51:49,531] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:51:49,531] [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
--------------------------------------------------------------------------------
[2023-06-19 08:51:49,533] [INFO] DFAST Taxonomy check result was written to GCA_018004645.1_ASM1800464v1_genomic.fna/tc_result.tsv
[2023-06-19 08:51:49,534] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:51:49,534] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:51:49,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb05d68b-dd64-4ba8-8cdf-662610865d41/dqc_reference/checkm_data
[2023-06-19 08:51:49,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:51:49,580] [INFO] Task started: CheckM
[2023-06-19 08:51:49,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018004645.1_ASM1800464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018004645.1_ASM1800464v1_genomic.fna/checkm_input GCA_018004645.1_ASM1800464v1_genomic.fna/checkm_result
[2023-06-19 08:52:36,042] [INFO] Task succeeded: CheckM
[2023-06-19 08:52:36,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:52:36,073] [INFO] ===== Completeness check finished =====
[2023-06-19 08:52:36,073] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:52:36,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018004645.1_ASM1800464v1_genomic.fna/markers.fasta)
[2023-06-19 08:52:36,074] [INFO] Task started: Blastn
[2023-06-19 08:52:36,075] [INFO] Running command: blastn -query GCA_018004645.1_ASM1800464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb05d68b-dd64-4ba8-8cdf-662610865d41/dqc_reference/reference_markers_gtdb.fasta -out GCA_018004645.1_ASM1800464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:52:36,815] [INFO] Task succeeded: Blastn
[2023-06-19 08:52:36,822] [INFO] Selected 24 target genomes.
[2023-06-19 08:52:36,822] [INFO] Target genome list was writen to GCA_018004645.1_ASM1800464v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:52:36,828] [INFO] Task started: fastANI
[2023-06-19 08:52:36,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a61107-113b-4955-8094-594b5d8b6f9b/GCA_018004645.1_ASM1800464v1_genomic.fna.gz --refList GCA_018004645.1_ASM1800464v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018004645.1_ASM1800464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:52:49,289] [INFO] Task succeeded: fastANI
[2023-06-19 08:52:49,294] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:52:49,294] [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_018004645.1	s__CAIWKO01 sp018004645	100.0	979	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CAIWKO01;g__CAIWKO01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-19 08:52:49,296] [INFO] GTDB search result was written to GCA_018004645.1_ASM1800464v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:52:49,297] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:52:49,303] [INFO] DFAST_QC result json was written to GCA_018004645.1_ASM1800464v1_genomic.fna/dqc_result.json
[2023-06-19 08:52:49,303] [INFO] DFAST_QC completed!
[2023-06-19 08:52:49,303] [INFO] Total running time: 0h1m33s