[2023-06-27 11:37:14,199] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:37:14,233] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:37:14,233] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c286f51-06df-4cc8-b18c-19680c9fa0a2/dqc_reference
[2023-06-27 11:37:15,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:37:15,691] [INFO] Task started: Prodigal
[2023-06-27 11:37:15,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg0233c5fc-76f1-4acf-85a5-3c409d2cf654/GCA_026993775.1_ASM2699377v1_genomic.fna.gz | prodigal -d GCA_026993775.1_ASM2699377v1_genomic.fna/cds.fna -a GCA_026993775.1_ASM2699377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:37:20,586] [INFO] Task succeeded: Prodigal
[2023-06-27 11:37:20,587] [INFO] Task started: HMMsearch
[2023-06-27 11:37:20,587] [INFO] Running command: hmmsearch --tblout GCA_026993775.1_ASM2699377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c286f51-06df-4cc8-b18c-19680c9fa0a2/dqc_reference/reference_markers.hmm GCA_026993775.1_ASM2699377v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:37:20,829] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:37:20,831] [INFO] Found 6/6 markers.
[2023-06-27 11:37:21,074] [INFO] Query marker FASTA was written to GCA_026993775.1_ASM2699377v1_genomic.fna/markers.fasta
[2023-06-27 11:37:21,075] [INFO] Task started: Blastn
[2023-06-27 11:37:21,075] [INFO] Running command: blastn -query GCA_026993775.1_ASM2699377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c286f51-06df-4cc8-b18c-19680c9fa0a2/dqc_reference/reference_markers.fasta -out GCA_026993775.1_ASM2699377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:37:21,805] [INFO] Task succeeded: Blastn
[2023-06-27 11:37:21,810] [INFO] Selected 38 target genomes.
[2023-06-27 11:37:21,811] [INFO] Target genome list was writen to GCA_026993775.1_ASM2699377v1_genomic.fna/target_genomes.txt
[2023-06-27 11:37:21,814] [INFO] Task started: fastANI
[2023-06-27 11:37:21,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg0233c5fc-76f1-4acf-85a5-3c409d2cf654/GCA_026993775.1_ASM2699377v1_genomic.fna.gz --refList GCA_026993775.1_ASM2699377v1_genomic.fna/target_genomes.txt --output GCA_026993775.1_ASM2699377v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:37:41,860] [INFO] Task succeeded: fastANI
[2023-06-27 11:37:41,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c286f51-06df-4cc8-b18c-19680c9fa0a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:37:41,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c286f51-06df-4cc8-b18c-19680c9fa0a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:37:41,863] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:37:41,863] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:37:41,863] [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 11:37:41,866] [INFO] DFAST Taxonomy check result was written to GCA_026993775.1_ASM2699377v1_genomic.fna/tc_result.tsv
[2023-06-27 11:37:41,867] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:37:41,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:37:41,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c286f51-06df-4cc8-b18c-19680c9fa0a2/dqc_reference/checkm_data
[2023-06-27 11:37:41,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:37:41,901] [INFO] Task started: CheckM
[2023-06-27 11:37:41,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026993775.1_ASM2699377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026993775.1_ASM2699377v1_genomic.fna/checkm_input GCA_026993775.1_ASM2699377v1_genomic.fna/checkm_result
[2023-06-27 11:38:04,819] [INFO] Task succeeded: CheckM
[2023-06-27 11:38:04,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 10.42%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-06-27 11:38:04,859] [INFO] ===== Completeness check finished =====
[2023-06-27 11:38:04,860] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:38:04,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026993775.1_ASM2699377v1_genomic.fna/markers.fasta)
[2023-06-27 11:38:04,861] [INFO] Task started: Blastn
[2023-06-27 11:38:04,861] [INFO] Running command: blastn -query GCA_026993775.1_ASM2699377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c286f51-06df-4cc8-b18c-19680c9fa0a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_026993775.1_ASM2699377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:38:05,954] [INFO] Task succeeded: Blastn
[2023-06-27 11:38:05,959] [INFO] Selected 29 target genomes.
[2023-06-27 11:38:05,959] [INFO] Target genome list was writen to GCA_026993775.1_ASM2699377v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:38:05,989] [INFO] Task started: fastANI
[2023-06-27 11:38:05,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg0233c5fc-76f1-4acf-85a5-3c409d2cf654/GCA_026993775.1_ASM2699377v1_genomic.fna.gz --refList GCA_026993775.1_ASM2699377v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026993775.1_ASM2699377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:38:18,665] [INFO] Task succeeded: fastANI
[2023-06-27 11:38:18,673] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:38:18,673] [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_015488295.1	s__GCA-2746365 sp015488295	76.9848	58	429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-229;f__SZUA-229;g__GCA-2746365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488885.1	s__S010-25 sp015488885	76.8379	74	429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-229;f__SZUA-229;g__S010-25	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:38:18,692] [INFO] GTDB search result was written to GCA_026993775.1_ASM2699377v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:38:18,693] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:38:18,698] [INFO] DFAST_QC result json was written to GCA_026993775.1_ASM2699377v1_genomic.fna/dqc_result.json
[2023-06-27 11:38:18,699] [INFO] DFAST_QC completed!
[2023-06-27 11:38:18,699] [INFO] Total running time: 0h1m5s