[2023-06-17 16:01:29,427] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:01:29,430] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:01:29,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d5155cf-48dc-47cf-9b76-1a907b6f0ef5/dqc_reference
[2023-06-17 16:01:30,980] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:01:30,981] [INFO] Task started: Prodigal
[2023-06-17 16:01:30,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg38a0d040-5db7-4811-8f67-dc9f48506561/GCA_028693885.1_ASM2869388v1_genomic.fna.gz | prodigal -d GCA_028693885.1_ASM2869388v1_genomic.fna/cds.fna -a GCA_028693885.1_ASM2869388v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:01:32,859] [INFO] Task succeeded: Prodigal
[2023-06-17 16:01:32,860] [INFO] Task started: HMMsearch
[2023-06-17 16:01:32,860] [INFO] Running command: hmmsearch --tblout GCA_028693885.1_ASM2869388v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d5155cf-48dc-47cf-9b76-1a907b6f0ef5/dqc_reference/reference_markers.hmm GCA_028693885.1_ASM2869388v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:01:33,088] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:01:33,089] [INFO] Found 6/6 markers.
[2023-06-17 16:01:33,106] [INFO] Query marker FASTA was written to GCA_028693885.1_ASM2869388v1_genomic.fna/markers.fasta
[2023-06-17 16:01:33,107] [INFO] Task started: Blastn
[2023-06-17 16:01:33,107] [INFO] Running command: blastn -query GCA_028693885.1_ASM2869388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5155cf-48dc-47cf-9b76-1a907b6f0ef5/dqc_reference/reference_markers.fasta -out GCA_028693885.1_ASM2869388v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:01:33,708] [INFO] Task succeeded: Blastn
[2023-06-17 16:01:33,712] [INFO] Selected 17 target genomes.
[2023-06-17 16:01:33,713] [INFO] Target genome list was writen to GCA_028693885.1_ASM2869388v1_genomic.fna/target_genomes.txt
[2023-06-17 16:01:33,718] [INFO] Task started: fastANI
[2023-06-17 16:01:33,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg38a0d040-5db7-4811-8f67-dc9f48506561/GCA_028693885.1_ASM2869388v1_genomic.fna.gz --refList GCA_028693885.1_ASM2869388v1_genomic.fna/target_genomes.txt --output GCA_028693885.1_ASM2869388v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:01:41,203] [INFO] Task succeeded: fastANI
[2023-06-17 16:01:41,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d5155cf-48dc-47cf-9b76-1a907b6f0ef5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:01:41,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d5155cf-48dc-47cf-9b76-1a907b6f0ef5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:01:41,205] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:01:41,205] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 16:01:41,205] [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
--------------------------------------------------------------------------------
[2023-06-17 16:01:41,208] [INFO] DFAST Taxonomy check result was written to GCA_028693885.1_ASM2869388v1_genomic.fna/tc_result.tsv
[2023-06-17 16:01:41,209] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:01:41,209] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:01:41,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d5155cf-48dc-47cf-9b76-1a907b6f0ef5/dqc_reference/checkm_data
[2023-06-17 16:01:41,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:01:41,236] [INFO] Task started: CheckM
[2023-06-17 16:01:41,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028693885.1_ASM2869388v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028693885.1_ASM2869388v1_genomic.fna/checkm_input GCA_028693885.1_ASM2869388v1_genomic.fna/checkm_result
[2023-06-17 16:01:56,652] [INFO] Task succeeded: CheckM
[2023-06-17 16:01:56,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 8.80%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-17 16:01:56,680] [INFO] ===== Completeness check finished =====
[2023-06-17 16:01:56,681] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:01:56,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028693885.1_ASM2869388v1_genomic.fna/markers.fasta)
[2023-06-17 16:01:56,682] [INFO] Task started: Blastn
[2023-06-17 16:01:56,682] [INFO] Running command: blastn -query GCA_028693885.1_ASM2869388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5155cf-48dc-47cf-9b76-1a907b6f0ef5/dqc_reference/reference_markers_gtdb.fasta -out GCA_028693885.1_ASM2869388v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:01:57,523] [INFO] Task succeeded: Blastn
[2023-06-17 16:01:57,527] [INFO] Selected 22 target genomes.
[2023-06-17 16:01:57,528] [INFO] Target genome list was writen to GCA_028693885.1_ASM2869388v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:01:57,549] [INFO] Task started: fastANI
[2023-06-17 16:01:57,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg38a0d040-5db7-4811-8f67-dc9f48506561/GCA_028693885.1_ASM2869388v1_genomic.fna.gz --refList GCA_028693885.1_ASM2869388v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028693885.1_ASM2869388v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:02:03,766] [INFO] Task succeeded: fastANI
[2023-06-17 16:02:03,769] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 16:02:03,769] [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
--------------------------------------------------------------------------------
[2023-06-17 16:02:03,772] [INFO] GTDB search result was written to GCA_028693885.1_ASM2869388v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:02:03,773] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:02:03,776] [INFO] DFAST_QC result json was written to GCA_028693885.1_ASM2869388v1_genomic.fna/dqc_result.json
[2023-06-17 16:02:03,776] [INFO] DFAST_QC completed!
[2023-06-17 16:02:03,776] [INFO] Total running time: 0h0m34s