[2023-06-27 02:26:16,206] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:26:16,215] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:26:16,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg286f18fb-91c8-461a-8346-4a294ff3b39a/dqc_reference
[2023-06-27 02:26:17,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:26:17,606] [INFO] Task started: Prodigal
[2023-06-27 02:26:17,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg9929f0fd-2f4d-422e-9f74-f3d548a57b27/GCA_026647715.1_ASM2664771v1_genomic.fna.gz | prodigal -d GCA_026647715.1_ASM2664771v1_genomic.fna/cds.fna -a GCA_026647715.1_ASM2664771v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:26:26,177] [INFO] Task succeeded: Prodigal
[2023-06-27 02:26:26,178] [INFO] Task started: HMMsearch
[2023-06-27 02:26:26,178] [INFO] Running command: hmmsearch --tblout GCA_026647715.1_ASM2664771v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg286f18fb-91c8-461a-8346-4a294ff3b39a/dqc_reference/reference_markers.hmm GCA_026647715.1_ASM2664771v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:26:26,429] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:26:26,431] [INFO] Found 6/6 markers.
[2023-06-27 02:26:26,467] [INFO] Query marker FASTA was written to GCA_026647715.1_ASM2664771v1_genomic.fna/markers.fasta
[2023-06-27 02:26:26,468] [INFO] Task started: Blastn
[2023-06-27 02:26:26,468] [INFO] Running command: blastn -query GCA_026647715.1_ASM2664771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg286f18fb-91c8-461a-8346-4a294ff3b39a/dqc_reference/reference_markers.fasta -out GCA_026647715.1_ASM2664771v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:26:27,232] [INFO] Task succeeded: Blastn
[2023-06-27 02:26:27,237] [INFO] Selected 16 target genomes.
[2023-06-27 02:26:27,237] [INFO] Target genome list was writen to GCA_026647715.1_ASM2664771v1_genomic.fna/target_genomes.txt
[2023-06-27 02:26:27,241] [INFO] Task started: fastANI
[2023-06-27 02:26:27,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg9929f0fd-2f4d-422e-9f74-f3d548a57b27/GCA_026647715.1_ASM2664771v1_genomic.fna.gz --refList GCA_026647715.1_ASM2664771v1_genomic.fna/target_genomes.txt --output GCA_026647715.1_ASM2664771v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:26:45,449] [INFO] Task succeeded: fastANI
[2023-06-27 02:26:45,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg286f18fb-91c8-461a-8346-4a294ff3b39a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:26:45,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg286f18fb-91c8-461a-8346-4a294ff3b39a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:26:45,452] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:26:45,452] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 02:26:45,452] [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 02:26:45,454] [INFO] DFAST Taxonomy check result was written to GCA_026647715.1_ASM2664771v1_genomic.fna/tc_result.tsv
[2023-06-27 02:26:45,455] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:26:45,455] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:26:45,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg286f18fb-91c8-461a-8346-4a294ff3b39a/dqc_reference/checkm_data
[2023-06-27 02:26:45,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:26:45,485] [INFO] Task started: CheckM
[2023-06-27 02:26:45,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026647715.1_ASM2664771v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026647715.1_ASM2664771v1_genomic.fna/checkm_input GCA_026647715.1_ASM2664771v1_genomic.fna/checkm_result
[2023-06-27 02:27:14,676] [INFO] Task succeeded: CheckM
[2023-06-27 02:27:14,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 02:27:14,697] [INFO] ===== Completeness check finished =====
[2023-06-27 02:27:14,698] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:27:14,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026647715.1_ASM2664771v1_genomic.fna/markers.fasta)
[2023-06-27 02:27:14,698] [INFO] Task started: Blastn
[2023-06-27 02:27:14,698] [INFO] Running command: blastn -query GCA_026647715.1_ASM2664771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg286f18fb-91c8-461a-8346-4a294ff3b39a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026647715.1_ASM2664771v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:27:15,607] [INFO] Task succeeded: Blastn
[2023-06-27 02:27:15,612] [INFO] Selected 17 target genomes.
[2023-06-27 02:27:15,612] [INFO] Target genome list was writen to GCA_026647715.1_ASM2664771v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:27:15,639] [INFO] Task started: fastANI
[2023-06-27 02:27:15,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg9929f0fd-2f4d-422e-9f74-f3d548a57b27/GCA_026647715.1_ASM2664771v1_genomic.fna.gz --refList GCA_026647715.1_ASM2664771v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026647715.1_ASM2664771v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:27:21,443] [INFO] Task succeeded: fastANI
[2023-06-27 02:27:21,448] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 02:27:21,448] [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_008363075.1	s__RHKK01 sp008363075	99.6565	336	412	d__Bacteria;p__Patescibacteria;c__ABY1;o__SG8-24;f__2-12-FULL-60-25;g__RHKK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-27 02:27:21,450] [INFO] GTDB search result was written to GCA_026647715.1_ASM2664771v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:27:21,451] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:27:21,454] [INFO] DFAST_QC result json was written to GCA_026647715.1_ASM2664771v1_genomic.fna/dqc_result.json
[2023-06-27 02:27:21,454] [INFO] DFAST_QC completed!
[2023-06-27 02:27:21,454] [INFO] Total running time: 0h1m5s