[2023-06-30 00:56:10,901] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:56:10,903] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:56:10,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg89f02496-904b-4c2c-aa1a-00ba074f1f2b/dqc_reference
[2023-06-30 00:56:12,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:56:12,151] [INFO] Task started: Prodigal
[2023-06-30 00:56:12,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg76dc58bc-4367-4437-b0ca-156ece512b5c/GCA_024682595.1_ASM2468259v1_genomic.fna.gz | prodigal -d GCA_024682595.1_ASM2468259v1_genomic.fna/cds.fna -a GCA_024682595.1_ASM2468259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:56:14,288] [INFO] Task succeeded: Prodigal
[2023-06-30 00:56:14,289] [INFO] Task started: HMMsearch
[2023-06-30 00:56:14,289] [INFO] Running command: hmmsearch --tblout GCA_024682595.1_ASM2468259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89f02496-904b-4c2c-aa1a-00ba074f1f2b/dqc_reference/reference_markers.hmm GCA_024682595.1_ASM2468259v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:56:14,501] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:56:14,503] [INFO] Found 6/6 markers.
[2023-06-30 00:56:14,524] [INFO] Query marker FASTA was written to GCA_024682595.1_ASM2468259v1_genomic.fna/markers.fasta
[2023-06-30 00:56:14,525] [INFO] Task started: Blastn
[2023-06-30 00:56:14,525] [INFO] Running command: blastn -query GCA_024682595.1_ASM2468259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89f02496-904b-4c2c-aa1a-00ba074f1f2b/dqc_reference/reference_markers.fasta -out GCA_024682595.1_ASM2468259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:15,124] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:15,129] [INFO] Selected 15 target genomes.
[2023-06-30 00:56:15,130] [INFO] Target genome list was writen to GCA_024682595.1_ASM2468259v1_genomic.fna/target_genomes.txt
[2023-06-30 00:56:15,132] [INFO] Task started: fastANI
[2023-06-30 00:56:15,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg76dc58bc-4367-4437-b0ca-156ece512b5c/GCA_024682595.1_ASM2468259v1_genomic.fna.gz --refList GCA_024682595.1_ASM2468259v1_genomic.fna/target_genomes.txt --output GCA_024682595.1_ASM2468259v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:56:22,737] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:22,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89f02496-904b-4c2c-aa1a-00ba074f1f2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:56:22,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89f02496-904b-4c2c-aa1a-00ba074f1f2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:56:22,739] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:56:22,739] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:56:22,740] [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
--------------------------------------------------------------------------------
[2023-06-30 00:56:22,741] [INFO] DFAST Taxonomy check result was written to GCA_024682595.1_ASM2468259v1_genomic.fna/tc_result.tsv
[2023-06-30 00:56:22,742] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:56:22,742] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:56:22,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89f02496-904b-4c2c-aa1a-00ba074f1f2b/dqc_reference/checkm_data
[2023-06-30 00:56:22,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:56:22,764] [INFO] Task started: CheckM
[2023-06-30 00:56:22,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024682595.1_ASM2468259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024682595.1_ASM2468259v1_genomic.fna/checkm_input GCA_024682595.1_ASM2468259v1_genomic.fna/checkm_result
[2023-06-30 00:56:37,502] [INFO] Task succeeded: CheckM
[2023-06-30 00:56:37,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 00:56:37,527] [INFO] ===== Completeness check finished =====
[2023-06-30 00:56:37,528] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:56:37,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024682595.1_ASM2468259v1_genomic.fna/markers.fasta)
[2023-06-30 00:56:37,528] [INFO] Task started: Blastn
[2023-06-30 00:56:37,529] [INFO] Running command: blastn -query GCA_024682595.1_ASM2468259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89f02496-904b-4c2c-aa1a-00ba074f1f2b/dqc_reference/reference_markers_gtdb.fasta -out GCA_024682595.1_ASM2468259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:38,325] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:38,330] [INFO] Selected 10 target genomes.
[2023-06-30 00:56:38,330] [INFO] Target genome list was writen to GCA_024682595.1_ASM2468259v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:56:38,333] [INFO] Task started: fastANI
[2023-06-30 00:56:38,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg76dc58bc-4367-4437-b0ca-156ece512b5c/GCA_024682595.1_ASM2468259v1_genomic.fna.gz --refList GCA_024682595.1_ASM2468259v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024682595.1_ASM2468259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:56:40,260] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:40,267] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:56:40,268] [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_016290315.1	s__UBA2834 sp016290315	94.7546	257	312	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002363515.1	s__UBA2834 sp002363515	92.5807	208	312	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	97.02	97.02	0.88	0.88	2	-
GCA_017540545.1	s__UBA2834 sp017540545	80.2828	97	312	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017964115.1	s__UBA2834 sp017964115	79.8057	101	312	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371895.1	s__UBA2834 sp002371895	78.0858	90	312	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437945.1	s__UBA2834 sp017437945	77.7473	72	312	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:56:40,270] [INFO] GTDB search result was written to GCA_024682595.1_ASM2468259v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:56:40,270] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:56:40,273] [INFO] DFAST_QC result json was written to GCA_024682595.1_ASM2468259v1_genomic.fna/dqc_result.json
[2023-06-30 00:56:40,273] [INFO] DFAST_QC completed!
[2023-06-30 00:56:40,273] [INFO] Total running time: 0h0m29s