[2023-06-18 22:24:56,105] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:24:56,143] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:24:56,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg63c90231-3f45-4765-9e56-fa145b38202d/dqc_reference
[2023-06-18 22:24:58,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:24:58,358] [INFO] Task started: Prodigal
[2023-06-18 22:24:58,359] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2ec1480-4328-48c2-8582-d5815ef8c29f/GCA_018606645.1_ASM1860664v1_genomic.fna.gz | prodigal -d GCA_018606645.1_ASM1860664v1_genomic.fna/cds.fna -a GCA_018606645.1_ASM1860664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:25:11,139] [INFO] Task succeeded: Prodigal
[2023-06-18 22:25:11,140] [INFO] Task started: HMMsearch
[2023-06-18 22:25:11,140] [INFO] Running command: hmmsearch --tblout GCA_018606645.1_ASM1860664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63c90231-3f45-4765-9e56-fa145b38202d/dqc_reference/reference_markers.hmm GCA_018606645.1_ASM1860664v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:25:11,438] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:25:11,440] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd2ec1480-4328-48c2-8582-d5815ef8c29f/GCA_018606645.1_ASM1860664v1_genomic.fna.gz]
[2023-06-18 22:25:11,477] [INFO] Query marker FASTA was written to GCA_018606645.1_ASM1860664v1_genomic.fna/markers.fasta
[2023-06-18 22:25:11,477] [INFO] Task started: Blastn
[2023-06-18 22:25:11,477] [INFO] Running command: blastn -query GCA_018606645.1_ASM1860664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63c90231-3f45-4765-9e56-fa145b38202d/dqc_reference/reference_markers.fasta -out GCA_018606645.1_ASM1860664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:25:12,153] [INFO] Task succeeded: Blastn
[2023-06-18 22:25:12,157] [INFO] Selected 15 target genomes.
[2023-06-18 22:25:12,157] [INFO] Target genome list was writen to GCA_018606645.1_ASM1860664v1_genomic.fna/target_genomes.txt
[2023-06-18 22:25:12,161] [INFO] Task started: fastANI
[2023-06-18 22:25:12,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ec1480-4328-48c2-8582-d5815ef8c29f/GCA_018606645.1_ASM1860664v1_genomic.fna.gz --refList GCA_018606645.1_ASM1860664v1_genomic.fna/target_genomes.txt --output GCA_018606645.1_ASM1860664v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:25:25,128] [INFO] Task succeeded: fastANI
[2023-06-18 22:25:25,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63c90231-3f45-4765-9e56-fa145b38202d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:25:25,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63c90231-3f45-4765-9e56-fa145b38202d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:25:25,131] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:25:25,131] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:25:25,132] [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
--------------------------------------------------------------------------------
[2023-06-18 22:25:25,134] [INFO] DFAST Taxonomy check result was written to GCA_018606645.1_ASM1860664v1_genomic.fna/tc_result.tsv
[2023-06-18 22:25:25,134] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:25:25,135] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:25:25,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63c90231-3f45-4765-9e56-fa145b38202d/dqc_reference/checkm_data
[2023-06-18 22:25:25,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:25:25,190] [INFO] Task started: CheckM
[2023-06-18 22:25:25,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018606645.1_ASM1860664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018606645.1_ASM1860664v1_genomic.fna/checkm_input GCA_018606645.1_ASM1860664v1_genomic.fna/checkm_result
[2023-06-18 22:26:04,679] [INFO] Task succeeded: CheckM
[2023-06-18 22:26:04,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:26:04,714] [INFO] ===== Completeness check finished =====
[2023-06-18 22:26:04,715] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:26:04,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018606645.1_ASM1860664v1_genomic.fna/markers.fasta)
[2023-06-18 22:26:04,716] [INFO] Task started: Blastn
[2023-06-18 22:26:04,716] [INFO] Running command: blastn -query GCA_018606645.1_ASM1860664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63c90231-3f45-4765-9e56-fa145b38202d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018606645.1_ASM1860664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:26:05,455] [INFO] Task succeeded: Blastn
[2023-06-18 22:26:05,460] [INFO] Selected 20 target genomes.
[2023-06-18 22:26:05,460] [INFO] Target genome list was writen to GCA_018606645.1_ASM1860664v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:26:05,486] [INFO] Task started: fastANI
[2023-06-18 22:26:05,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ec1480-4328-48c2-8582-d5815ef8c29f/GCA_018606645.1_ASM1860664v1_genomic.fna.gz --refList GCA_018606645.1_ASM1860664v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018606645.1_ASM1860664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:26:16,756] [INFO] Task succeeded: fastANI
[2023-06-18 22:26:16,763] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:26:16,763] [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_018606645.1	s__TumbabinsA96 sp018606645	100.0	1406	1407	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__JAAYZQ01;f__JAAYZQ01;g__TumbabinsA96	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016926595.1	s__JAFGOG01 sp016926595	76.4668	159	1407	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__JAAYZQ01;f__JAAYZQ01;g__JAFGOG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016929795.1	s__JAFGIA01 sp016929795	75.8249	131	1407	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__JAAYZQ01;f__JAAYZQ01;g__JAFGIA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:26:16,767] [INFO] GTDB search result was written to GCA_018606645.1_ASM1860664v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:26:16,768] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:26:16,770] [INFO] DFAST_QC result json was written to GCA_018606645.1_ASM1860664v1_genomic.fna/dqc_result.json
[2023-06-18 22:26:16,771] [INFO] DFAST_QC completed!
[2023-06-18 22:26:16,771] [INFO] Total running time: 0h1m21s