[2023-06-16 22:22:53,154] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:22:53,157] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:22:53,157] [INFO] DQC Reference Directory: /var/lib/cwl/stgb46b10be-563a-40ad-86ee-57cf80520cf7/dqc_reference
[2023-06-16 22:22:54,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:22:54,678] [INFO] Task started: Prodigal
[2023-06-16 22:22:54,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg70457bd7-581e-419c-bb50-14de13af3849/GCA_013286175.1_ASM1328617v1_genomic.fna.gz | prodigal -d GCA_013286175.1_ASM1328617v1_genomic.fna/cds.fna -a GCA_013286175.1_ASM1328617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:22:57,060] [INFO] Task succeeded: Prodigal
[2023-06-16 22:22:57,060] [INFO] Task started: HMMsearch
[2023-06-16 22:22:57,060] [INFO] Running command: hmmsearch --tblout GCA_013286175.1_ASM1328617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb46b10be-563a-40ad-86ee-57cf80520cf7/dqc_reference/reference_markers.hmm GCA_013286175.1_ASM1328617v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:22:57,329] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:22:57,330] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg70457bd7-581e-419c-bb50-14de13af3849/GCA_013286175.1_ASM1328617v1_genomic.fna.gz]
[2023-06-16 22:22:57,361] [INFO] Query marker FASTA was written to GCA_013286175.1_ASM1328617v1_genomic.fna/markers.fasta
[2023-06-16 22:22:57,362] [INFO] Task started: Blastn
[2023-06-16 22:22:57,362] [INFO] Running command: blastn -query GCA_013286175.1_ASM1328617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb46b10be-563a-40ad-86ee-57cf80520cf7/dqc_reference/reference_markers.fasta -out GCA_013286175.1_ASM1328617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:22:58,086] [INFO] Task succeeded: Blastn
[2023-06-16 22:22:58,089] [INFO] Selected 19 target genomes.
[2023-06-16 22:22:58,090] [INFO] Target genome list was writen to GCA_013286175.1_ASM1328617v1_genomic.fna/target_genomes.txt
[2023-06-16 22:22:58,101] [INFO] Task started: fastANI
[2023-06-16 22:22:58,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg70457bd7-581e-419c-bb50-14de13af3849/GCA_013286175.1_ASM1328617v1_genomic.fna.gz --refList GCA_013286175.1_ASM1328617v1_genomic.fna/target_genomes.txt --output GCA_013286175.1_ASM1328617v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:23:07,325] [INFO] Task succeeded: fastANI
[2023-06-16 22:23:07,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb46b10be-563a-40ad-86ee-57cf80520cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:23:07,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb46b10be-563a-40ad-86ee-57cf80520cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:23:07,327] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:23:07,328] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 22:23:07,328] [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
--------------------------------------------------------------------------------
[2023-06-16 22:23:07,330] [INFO] DFAST Taxonomy check result was written to GCA_013286175.1_ASM1328617v1_genomic.fna/tc_result.tsv
[2023-06-16 22:23:07,330] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:23:07,331] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:23:07,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb46b10be-563a-40ad-86ee-57cf80520cf7/dqc_reference/checkm_data
[2023-06-16 22:23:07,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:23:07,353] [INFO] Task started: CheckM
[2023-06-16 22:23:07,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013286175.1_ASM1328617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013286175.1_ASM1328617v1_genomic.fna/checkm_input GCA_013286175.1_ASM1328617v1_genomic.fna/checkm_result
[2023-06-16 22:23:23,160] [INFO] Task succeeded: CheckM
[2023-06-16 22:23:23,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:23:23,185] [INFO] ===== Completeness check finished =====
[2023-06-16 22:23:23,186] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:23:23,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013286175.1_ASM1328617v1_genomic.fna/markers.fasta)
[2023-06-16 22:23:23,186] [INFO] Task started: Blastn
[2023-06-16 22:23:23,186] [INFO] Running command: blastn -query GCA_013286175.1_ASM1328617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb46b10be-563a-40ad-86ee-57cf80520cf7/dqc_reference/reference_markers_gtdb.fasta -out GCA_013286175.1_ASM1328617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:23:24,107] [INFO] Task succeeded: Blastn
[2023-06-16 22:23:24,112] [INFO] Selected 22 target genomes.
[2023-06-16 22:23:24,112] [INFO] Target genome list was writen to GCA_013286175.1_ASM1328617v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:23:24,142] [INFO] Task started: fastANI
[2023-06-16 22:23:24,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg70457bd7-581e-419c-bb50-14de13af3849/GCA_013286175.1_ASM1328617v1_genomic.fna.gz --refList GCA_013286175.1_ASM1328617v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013286175.1_ASM1328617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:23:34,185] [INFO] Task succeeded: fastANI
[2023-06-16 22:23:34,188] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:23:34,189] [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_013289605.1	s__JABCZS01 sp013289605	99.02	260	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JABCZS01;f__JABCZS01;g__JABCZS01	95.0	99.02	99.02	0.78	0.78	3	conclusive
GCA_013289085.1	s__JABCZS01 sp013289085	77.4567	59	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JABCZS01;f__JABCZS01;g__JABCZS01	95.0	99.93	99.93	0.62	0.62	2	-
--------------------------------------------------------------------------------
[2023-06-16 22:23:34,191] [INFO] GTDB search result was written to GCA_013286175.1_ASM1328617v1_genomic.fna/result_gtdb.tsv
[2023-06-16 22:23:34,191] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:23:34,193] [INFO] DFAST_QC result json was written to GCA_013286175.1_ASM1328617v1_genomic.fna/dqc_result.json
[2023-06-16 22:23:34,193] [INFO] DFAST_QC completed!
[2023-06-16 22:23:34,194] [INFO] Total running time: 0h0m41s