[2023-06-27 01:35:17,706] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:35:17,716] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:35:17,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg89f801e4-f57f-43e1-b609-4f075ff960d6/dqc_reference
[2023-06-27 01:35:18,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:35:18,963] [INFO] Task started: Prodigal
[2023-06-27 01:35:18,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0c177e7-959c-4ef4-86a4-58385fbfa65d/GCA_026416095.1_ASM2641609v1_genomic.fna.gz | prodigal -d GCA_026416095.1_ASM2641609v1_genomic.fna/cds.fna -a GCA_026416095.1_ASM2641609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:35:25,568] [INFO] Task succeeded: Prodigal
[2023-06-27 01:35:25,569] [INFO] Task started: HMMsearch
[2023-06-27 01:35:25,569] [INFO] Running command: hmmsearch --tblout GCA_026416095.1_ASM2641609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89f801e4-f57f-43e1-b609-4f075ff960d6/dqc_reference/reference_markers.hmm GCA_026416095.1_ASM2641609v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:35:25,851] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:35:25,852] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd0c177e7-959c-4ef4-86a4-58385fbfa65d/GCA_026416095.1_ASM2641609v1_genomic.fna.gz]
[2023-06-27 01:35:25,876] [INFO] Query marker FASTA was written to GCA_026416095.1_ASM2641609v1_genomic.fna/markers.fasta
[2023-06-27 01:35:25,877] [INFO] Task started: Blastn
[2023-06-27 01:35:25,877] [INFO] Running command: blastn -query GCA_026416095.1_ASM2641609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89f801e4-f57f-43e1-b609-4f075ff960d6/dqc_reference/reference_markers.fasta -out GCA_026416095.1_ASM2641609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:35:26,504] [INFO] Task succeeded: Blastn
[2023-06-27 01:35:26,508] [INFO] Selected 28 target genomes.
[2023-06-27 01:35:26,509] [INFO] Target genome list was writen to GCA_026416095.1_ASM2641609v1_genomic.fna/target_genomes.txt
[2023-06-27 01:35:26,514] [INFO] Task started: fastANI
[2023-06-27 01:35:26,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0c177e7-959c-4ef4-86a4-58385fbfa65d/GCA_026416095.1_ASM2641609v1_genomic.fna.gz --refList GCA_026416095.1_ASM2641609v1_genomic.fna/target_genomes.txt --output GCA_026416095.1_ASM2641609v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 01:35:44,479] [INFO] Task succeeded: fastANI
[2023-06-27 01:35:44,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89f801e4-f57f-43e1-b609-4f075ff960d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 01:35:44,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89f801e4-f57f-43e1-b609-4f075ff960d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 01:35:44,482] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 01:35:44,482] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 01:35:44,482] [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
--------------------------------------------------------------------------------
[2023-06-27 01:35:44,484] [INFO] DFAST Taxonomy check result was written to GCA_026416095.1_ASM2641609v1_genomic.fna/tc_result.tsv
[2023-06-27 01:35:44,485] [INFO] ===== Taxonomy check completed =====
[2023-06-27 01:35:44,485] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:35:44,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89f801e4-f57f-43e1-b609-4f075ff960d6/dqc_reference/checkm_data
[2023-06-27 01:35:44,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:35:44,516] [INFO] Task started: CheckM
[2023-06-27 01:35:44,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026416095.1_ASM2641609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026416095.1_ASM2641609v1_genomic.fna/checkm_input GCA_026416095.1_ASM2641609v1_genomic.fna/checkm_result
[2023-06-27 01:36:10,020] [INFO] Task succeeded: CheckM
[2023-06-27 01:36:10,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:36:10,044] [INFO] ===== Completeness check finished =====
[2023-06-27 01:36:10,044] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:36:10,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026416095.1_ASM2641609v1_genomic.fna/markers.fasta)
[2023-06-27 01:36:10,045] [INFO] Task started: Blastn
[2023-06-27 01:36:10,045] [INFO] Running command: blastn -query GCA_026416095.1_ASM2641609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89f801e4-f57f-43e1-b609-4f075ff960d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_026416095.1_ASM2641609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:36:10,959] [INFO] Task succeeded: Blastn
[2023-06-27 01:36:10,964] [INFO] Selected 29 target genomes.
[2023-06-27 01:36:10,964] [INFO] Target genome list was writen to GCA_026416095.1_ASM2641609v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:36:10,988] [INFO] Task started: fastANI
[2023-06-27 01:36:10,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0c177e7-959c-4ef4-86a4-58385fbfa65d/GCA_026416095.1_ASM2641609v1_genomic.fna.gz --refList GCA_026416095.1_ASM2641609v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026416095.1_ASM2641609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:36:25,969] [INFO] Task succeeded: fastANI
[2023-06-27 01:36:25,975] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:36:25,975] [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_001769035.1	s__GWA2-32-17 sp001769035	74.8582	65	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWA2-32-17;g__GWA2-32-17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002084355.1	s__4572-128 sp002084355	74.6988	91	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4572-128;g__4572-128	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 01:36:25,977] [INFO] GTDB search result was written to GCA_026416095.1_ASM2641609v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:36:25,978] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:36:25,980] [INFO] DFAST_QC result json was written to GCA_026416095.1_ASM2641609v1_genomic.fna/dqc_result.json
[2023-06-27 01:36:25,981] [INFO] DFAST_QC completed!
[2023-06-27 01:36:25,981] [INFO] Total running time: 0h1m8s