[2023-06-27 11:39:43,440] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:39:43,450] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:39:43,451] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaa7c6fe-da1a-4e54-891d-c6093a00a05f/dqc_reference
[2023-06-27 11:39:44,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:39:44,905] [INFO] Task started: Prodigal
[2023-06-27 11:39:44,905] [INFO] Running command: gunzip -c /var/lib/cwl/stgee0f80a5-7ff7-4d35-b9d4-aaf445d694fc/GCA_026983995.1_ASM2698399v1_genomic.fna.gz | prodigal -d GCA_026983995.1_ASM2698399v1_genomic.fna/cds.fna -a GCA_026983995.1_ASM2698399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:39:48,330] [INFO] Task succeeded: Prodigal
[2023-06-27 11:39:48,331] [INFO] Task started: HMMsearch
[2023-06-27 11:39:48,331] [INFO] Running command: hmmsearch --tblout GCA_026983995.1_ASM2698399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaa7c6fe-da1a-4e54-891d-c6093a00a05f/dqc_reference/reference_markers.hmm GCA_026983995.1_ASM2698399v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:39:48,550] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:39:48,552] [INFO] Found 6/6 markers.
[2023-06-27 11:39:48,579] [INFO] Query marker FASTA was written to GCA_026983995.1_ASM2698399v1_genomic.fna/markers.fasta
[2023-06-27 11:39:48,580] [INFO] Task started: Blastn
[2023-06-27 11:39:48,580] [INFO] Running command: blastn -query GCA_026983995.1_ASM2698399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaa7c6fe-da1a-4e54-891d-c6093a00a05f/dqc_reference/reference_markers.fasta -out GCA_026983995.1_ASM2698399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:39:49,192] [INFO] Task succeeded: Blastn
[2023-06-27 11:39:49,197] [INFO] Selected 22 target genomes.
[2023-06-27 11:39:49,198] [INFO] Target genome list was writen to GCA_026983995.1_ASM2698399v1_genomic.fna/target_genomes.txt
[2023-06-27 11:39:49,224] [INFO] Task started: fastANI
[2023-06-27 11:39:49,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgee0f80a5-7ff7-4d35-b9d4-aaf445d694fc/GCA_026983995.1_ASM2698399v1_genomic.fna.gz --refList GCA_026983995.1_ASM2698399v1_genomic.fna/target_genomes.txt --output GCA_026983995.1_ASM2698399v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:39:55,724] [INFO] Task succeeded: fastANI
[2023-06-27 11:39:55,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaa7c6fe-da1a-4e54-891d-c6093a00a05f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:39:55,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaa7c6fe-da1a-4e54-891d-c6093a00a05f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:39:55,727] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:39:55,727] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:39:55,727] [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 11:39:55,729] [INFO] DFAST Taxonomy check result was written to GCA_026983995.1_ASM2698399v1_genomic.fna/tc_result.tsv
[2023-06-27 11:39:55,730] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:39:55,731] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:39:55,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaa7c6fe-da1a-4e54-891d-c6093a00a05f/dqc_reference/checkm_data
[2023-06-27 11:39:55,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:39:55,764] [INFO] Task started: CheckM
[2023-06-27 11:39:55,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026983995.1_ASM2698399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026983995.1_ASM2698399v1_genomic.fna/checkm_input GCA_026983995.1_ASM2698399v1_genomic.fna/checkm_result
[2023-06-27 11:40:15,091] [INFO] Task succeeded: CheckM
[2023-06-27 11:40:15,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:40:15,142] [INFO] ===== Completeness check finished =====
[2023-06-27 11:40:15,143] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:40:15,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026983995.1_ASM2698399v1_genomic.fna/markers.fasta)
[2023-06-27 11:40:15,143] [INFO] Task started: Blastn
[2023-06-27 11:40:15,144] [INFO] Running command: blastn -query GCA_026983995.1_ASM2698399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaa7c6fe-da1a-4e54-891d-c6093a00a05f/dqc_reference/reference_markers_gtdb.fasta -out GCA_026983995.1_ASM2698399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:40:16,028] [INFO] Task succeeded: Blastn
[2023-06-27 11:40:16,031] [INFO] Selected 23 target genomes.
[2023-06-27 11:40:16,031] [INFO] Target genome list was writen to GCA_026983995.1_ASM2698399v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:40:16,039] [INFO] Task started: fastANI
[2023-06-27 11:40:16,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgee0f80a5-7ff7-4d35-b9d4-aaf445d694fc/GCA_026983995.1_ASM2698399v1_genomic.fna.gz --refList GCA_026983995.1_ASM2698399v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026983995.1_ASM2698399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:40:23,969] [INFO] Task succeeded: fastANI
[2023-06-27 11:40:23,978] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:40:23,978] [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_015662615.1	s__SZUA-1433 sp015662615	77.4761	57	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__QNZT01;g__SZUA-1433	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744895.1	s__SZUA-1433 sp016744895	77.4188	91	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__QNZT01;g__SZUA-1433	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978455.1	s__QNZT01 sp003978455	77.0297	52	397	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__QNZT01;g__QNZT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:40:23,981] [INFO] GTDB search result was written to GCA_026983995.1_ASM2698399v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:40:23,981] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:40:23,996] [INFO] DFAST_QC result json was written to GCA_026983995.1_ASM2698399v1_genomic.fna/dqc_result.json
[2023-06-27 11:40:23,996] [INFO] DFAST_QC completed!
[2023-06-27 11:40:23,996] [INFO] Total running time: 0h0m41s