[2023-06-19 08:40:04,008] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:40:04,013] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:40:04,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b8aadec-1e53-4302-bdd3-85bd6e7b7897/dqc_reference
[2023-06-19 08:40:05,234] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:40:05,235] [INFO] Task started: Prodigal
[2023-06-19 08:40:05,235] [INFO] Running command: gunzip -c /var/lib/cwl/stg83e20be8-bf0a-496b-bdff-f2e53f4590f4/GCA_018664665.1_ASM1866466v1_genomic.fna.gz | prodigal -d GCA_018664665.1_ASM1866466v1_genomic.fna/cds.fna -a GCA_018664665.1_ASM1866466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:40:09,048] [INFO] Task succeeded: Prodigal
[2023-06-19 08:40:09,049] [INFO] Task started: HMMsearch
[2023-06-19 08:40:09,049] [INFO] Running command: hmmsearch --tblout GCA_018664665.1_ASM1866466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b8aadec-1e53-4302-bdd3-85bd6e7b7897/dqc_reference/reference_markers.hmm GCA_018664665.1_ASM1866466v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:40:09,249] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:40:09,250] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg83e20be8-bf0a-496b-bdff-f2e53f4590f4/GCA_018664665.1_ASM1866466v1_genomic.fna.gz]
[2023-06-19 08:40:09,276] [INFO] Query marker FASTA was written to GCA_018664665.1_ASM1866466v1_genomic.fna/markers.fasta
[2023-06-19 08:40:09,276] [INFO] Task started: Blastn
[2023-06-19 08:40:09,276] [INFO] Running command: blastn -query GCA_018664665.1_ASM1866466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b8aadec-1e53-4302-bdd3-85bd6e7b7897/dqc_reference/reference_markers.fasta -out GCA_018664665.1_ASM1866466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:09,890] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:09,895] [INFO] Selected 17 target genomes.
[2023-06-19 08:40:09,896] [INFO] Target genome list was writen to GCA_018664665.1_ASM1866466v1_genomic.fna/target_genomes.txt
[2023-06-19 08:40:09,898] [INFO] Task started: fastANI
[2023-06-19 08:40:09,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e20be8-bf0a-496b-bdff-f2e53f4590f4/GCA_018664665.1_ASM1866466v1_genomic.fna.gz --refList GCA_018664665.1_ASM1866466v1_genomic.fna/target_genomes.txt --output GCA_018664665.1_ASM1866466v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:40:20,667] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:20,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b8aadec-1e53-4302-bdd3-85bd6e7b7897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:40:20,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b8aadec-1e53-4302-bdd3-85bd6e7b7897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:40:20,669] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:40:20,669] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:40:20,669] [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
--------------------------------------------------------------------------------
[2023-06-19 08:40:20,671] [INFO] DFAST Taxonomy check result was written to GCA_018664665.1_ASM1866466v1_genomic.fna/tc_result.tsv
[2023-06-19 08:40:20,673] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:40:20,673] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:40:20,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b8aadec-1e53-4302-bdd3-85bd6e7b7897/dqc_reference/checkm_data
[2023-06-19 08:40:20,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:40:20,706] [INFO] Task started: CheckM
[2023-06-19 08:40:20,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018664665.1_ASM1866466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018664665.1_ASM1866466v1_genomic.fna/checkm_input GCA_018664665.1_ASM1866466v1_genomic.fna/checkm_result
[2023-06-19 08:40:40,621] [INFO] Task succeeded: CheckM
[2023-06-19 08:40:40,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.02%
Contamintation: 6.17%
Strain heterogeneity: 46.15%
--------------------------------------------------------------------------------
[2023-06-19 08:40:40,645] [INFO] ===== Completeness check finished =====
[2023-06-19 08:40:40,645] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:40:40,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018664665.1_ASM1866466v1_genomic.fna/markers.fasta)
[2023-06-19 08:40:40,646] [INFO] Task started: Blastn
[2023-06-19 08:40:40,646] [INFO] Running command: blastn -query GCA_018664665.1_ASM1866466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b8aadec-1e53-4302-bdd3-85bd6e7b7897/dqc_reference/reference_markers_gtdb.fasta -out GCA_018664665.1_ASM1866466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:41,337] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:41,341] [INFO] Selected 16 target genomes.
[2023-06-19 08:40:41,341] [INFO] Target genome list was writen to GCA_018664665.1_ASM1866466v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:40:41,345] [INFO] Task started: fastANI
[2023-06-19 08:40:41,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e20be8-bf0a-496b-bdff-f2e53f4590f4/GCA_018664665.1_ASM1866466v1_genomic.fna.gz --refList GCA_018664665.1_ASM1866466v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018664665.1_ASM1866466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:40:51,752] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:51,756] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:40:51,756] [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_002292215.1	s__Glaciecola sp002292215	95.687	354	391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.49	98.83	0.91	0.88	4	conclusive
GCF_000155775.1	s__Glaciecola sp000155775	78.7829	135	391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:40:51,760] [INFO] GTDB search result was written to GCA_018664665.1_ASM1866466v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:40:51,761] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:40:51,764] [INFO] DFAST_QC result json was written to GCA_018664665.1_ASM1866466v1_genomic.fna/dqc_result.json
[2023-06-19 08:40:51,764] [INFO] DFAST_QC completed!
[2023-06-19 08:40:51,764] [INFO] Total running time: 0h0m48s