[2023-06-13 14:34:05,990] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:34:06,018] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:34:06,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg623d915e-9f64-43cb-af7d-959e3bfb759a/dqc_reference
[2023-06-13 14:34:07,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:34:07,223] [INFO] Task started: Prodigal
[2023-06-13 14:34:07,223] [INFO] Running command: gunzip -c /var/lib/cwl/stgb837f0ec-b4e7-41df-a378-9f448a789441/GCA_022769005.1_ASM2276900v1_genomic.fna.gz | prodigal -d GCA_022769005.1_ASM2276900v1_genomic.fna/cds.fna -a GCA_022769005.1_ASM2276900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:34:10,244] [INFO] Task succeeded: Prodigal
[2023-06-13 14:34:10,245] [INFO] Task started: HMMsearch
[2023-06-13 14:34:10,245] [INFO] Running command: hmmsearch --tblout GCA_022769005.1_ASM2276900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg623d915e-9f64-43cb-af7d-959e3bfb759a/dqc_reference/reference_markers.hmm GCA_022769005.1_ASM2276900v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:34:10,477] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:34:10,479] [INFO] Found 6/6 markers.
[2023-06-13 14:34:10,502] [INFO] Query marker FASTA was written to GCA_022769005.1_ASM2276900v1_genomic.fna/markers.fasta
[2023-06-13 14:34:10,503] [INFO] Task started: Blastn
[2023-06-13 14:34:10,503] [INFO] Running command: blastn -query GCA_022769005.1_ASM2276900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623d915e-9f64-43cb-af7d-959e3bfb759a/dqc_reference/reference_markers.fasta -out GCA_022769005.1_ASM2276900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:34:11,123] [INFO] Task succeeded: Blastn
[2023-06-13 14:34:11,127] [INFO] Selected 19 target genomes.
[2023-06-13 14:34:11,128] [INFO] Target genome list was writen to GCA_022769005.1_ASM2276900v1_genomic.fna/target_genomes.txt
[2023-06-13 14:34:11,130] [INFO] Task started: fastANI
[2023-06-13 14:34:11,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgb837f0ec-b4e7-41df-a378-9f448a789441/GCA_022769005.1_ASM2276900v1_genomic.fna.gz --refList GCA_022769005.1_ASM2276900v1_genomic.fna/target_genomes.txt --output GCA_022769005.1_ASM2276900v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:34:20,149] [INFO] Task succeeded: fastANI
[2023-06-13 14:34:20,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg623d915e-9f64-43cb-af7d-959e3bfb759a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:34:20,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg623d915e-9f64-43cb-af7d-959e3bfb759a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:34:20,152] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:34:20,152] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 14:34:20,152] [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
--------------------------------------------------------------------------------
[2023-06-13 14:34:20,155] [INFO] DFAST Taxonomy check result was written to GCA_022769005.1_ASM2276900v1_genomic.fna/tc_result.tsv
[2023-06-13 14:34:20,156] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:34:20,156] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:34:20,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg623d915e-9f64-43cb-af7d-959e3bfb759a/dqc_reference/checkm_data
[2023-06-13 14:34:20,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:34:20,182] [INFO] Task started: CheckM
[2023-06-13 14:34:20,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022769005.1_ASM2276900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022769005.1_ASM2276900v1_genomic.fna/checkm_input GCA_022769005.1_ASM2276900v1_genomic.fna/checkm_result
[2023-06-13 14:34:37,446] [INFO] Task succeeded: CheckM
[2023-06-13 14:34:37,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:34:37,467] [INFO] ===== Completeness check finished =====
[2023-06-13 14:34:37,468] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:34:37,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022769005.1_ASM2276900v1_genomic.fna/markers.fasta)
[2023-06-13 14:34:37,468] [INFO] Task started: Blastn
[2023-06-13 14:34:37,469] [INFO] Running command: blastn -query GCA_022769005.1_ASM2276900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623d915e-9f64-43cb-af7d-959e3bfb759a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022769005.1_ASM2276900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:34:38,475] [INFO] Task succeeded: Blastn
[2023-06-13 14:34:38,481] [INFO] Selected 30 target genomes.
[2023-06-13 14:34:38,482] [INFO] Target genome list was writen to GCA_022769005.1_ASM2276900v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:34:38,523] [INFO] Task started: fastANI
[2023-06-13 14:34:38,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgb837f0ec-b4e7-41df-a378-9f448a789441/GCA_022769005.1_ASM2276900v1_genomic.fna.gz --refList GCA_022769005.1_ASM2276900v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022769005.1_ASM2276900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:34:49,969] [INFO] Task succeeded: fastANI
[2023-06-13 14:34:49,973] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:34:49,973] [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_900545225.1	s__UBA4285 sp900545225	81.9186	332	468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA4285	95.0	99.15	99.11	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-13 14:34:49,975] [INFO] GTDB search result was written to GCA_022769005.1_ASM2276900v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:34:49,976] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:34:49,978] [INFO] DFAST_QC result json was written to GCA_022769005.1_ASM2276900v1_genomic.fna/dqc_result.json
[2023-06-13 14:34:49,978] [INFO] DFAST_QC completed!
[2023-06-13 14:34:49,978] [INFO] Total running time: 0h0m44s