[2023-06-29 19:44:46,834] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:44:46,837] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:44:46,837] [INFO] DQC Reference Directory: /var/lib/cwl/stgce7aa6ed-f268-4028-b50b-33f254f213ea/dqc_reference
[2023-06-29 19:44:50,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:44:50,092] [INFO] Task started: Prodigal
[2023-06-29 19:44:50,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ea86c4b-7976-4f8e-a2cb-5f9749b802e7/GCA_023429135.1_ASM2342913v1_genomic.fna.gz | prodigal -d GCA_023429135.1_ASM2342913v1_genomic.fna/cds.fna -a GCA_023429135.1_ASM2342913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:45:18,497] [INFO] Task succeeded: Prodigal
[2023-06-29 19:45:18,497] [INFO] Task started: HMMsearch
[2023-06-29 19:45:18,498] [INFO] Running command: hmmsearch --tblout GCA_023429135.1_ASM2342913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce7aa6ed-f268-4028-b50b-33f254f213ea/dqc_reference/reference_markers.hmm GCA_023429135.1_ASM2342913v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:45:18,860] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:45:18,862] [INFO] Found 6/6 markers.
[2023-06-29 19:45:18,918] [INFO] Query marker FASTA was written to GCA_023429135.1_ASM2342913v1_genomic.fna/markers.fasta
[2023-06-29 19:45:18,918] [INFO] Task started: Blastn
[2023-06-29 19:45:18,919] [INFO] Running command: blastn -query GCA_023429135.1_ASM2342913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce7aa6ed-f268-4028-b50b-33f254f213ea/dqc_reference/reference_markers.fasta -out GCA_023429135.1_ASM2342913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:45:19,521] [INFO] Task succeeded: Blastn
[2023-06-29 19:45:19,527] [INFO] Selected 26 target genomes.
[2023-06-29 19:45:19,528] [INFO] Target genome list was writen to GCA_023429135.1_ASM2342913v1_genomic.fna/target_genomes.txt
[2023-06-29 19:45:19,541] [INFO] Task started: fastANI
[2023-06-29 19:45:19,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea86c4b-7976-4f8e-a2cb-5f9749b802e7/GCA_023429135.1_ASM2342913v1_genomic.fna.gz --refList GCA_023429135.1_ASM2342913v1_genomic.fna/target_genomes.txt --output GCA_023429135.1_ASM2342913v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:45:36,674] [INFO] Task succeeded: fastANI
[2023-06-29 19:45:36,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce7aa6ed-f268-4028-b50b-33f254f213ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:45:36,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce7aa6ed-f268-4028-b50b-33f254f213ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:45:36,677] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:45:36,677] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:45:36,677] [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 19:45:36,680] [INFO] DFAST Taxonomy check result was written to GCA_023429135.1_ASM2342913v1_genomic.fna/tc_result.tsv
[2023-06-29 19:45:36,681] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:45:36,681] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:45:36,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce7aa6ed-f268-4028-b50b-33f254f213ea/dqc_reference/checkm_data
[2023-06-29 19:45:36,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:45:36,754] [INFO] Task started: CheckM
[2023-06-29 19:45:36,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023429135.1_ASM2342913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023429135.1_ASM2342913v1_genomic.fna/checkm_input GCA_023429135.1_ASM2342913v1_genomic.fna/checkm_result
[2023-06-29 19:46:55,710] [INFO] Task succeeded: CheckM
[2023-06-29 19:46:55,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:46:55,734] [INFO] ===== Completeness check finished =====
[2023-06-29 19:46:55,735] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:46:55,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023429135.1_ASM2342913v1_genomic.fna/markers.fasta)
[2023-06-29 19:46:55,735] [INFO] Task started: Blastn
[2023-06-29 19:46:55,735] [INFO] Running command: blastn -query GCA_023429135.1_ASM2342913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce7aa6ed-f268-4028-b50b-33f254f213ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_023429135.1_ASM2342913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:46:56,512] [INFO] Task succeeded: Blastn
[2023-06-29 19:46:56,517] [INFO] Selected 32 target genomes.
[2023-06-29 19:46:56,517] [INFO] Target genome list was writen to GCA_023429135.1_ASM2342913v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:46:56,526] [INFO] Task started: fastANI
[2023-06-29 19:46:56,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea86c4b-7976-4f8e-a2cb-5f9749b802e7/GCA_023429135.1_ASM2342913v1_genomic.fna.gz --refList GCA_023429135.1_ASM2342913v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023429135.1_ASM2342913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:47:18,162] [INFO] Task succeeded: fastANI
[2023-06-29 19:47:18,167] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:47:18,168] [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_012031335.1	s__JAAUTT01 sp012031335	78.056	283	2347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JAAUTT01;g__JAAUTT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:47:18,170] [INFO] GTDB search result was written to GCA_023429135.1_ASM2342913v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:47:18,170] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:47:18,172] [INFO] DFAST_QC result json was written to GCA_023429135.1_ASM2342913v1_genomic.fna/dqc_result.json
[2023-06-29 19:47:18,173] [INFO] DFAST_QC completed!
[2023-06-29 19:47:18,173] [INFO] Total running time: 0h2m31s