[2023-06-28 04:59:06,059] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:59:06,061] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:59:06,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg74de53e3-77ef-494f-983b-70936578aaa1/dqc_reference
[2023-06-28 04:59:07,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:59:07,472] [INFO] Task started: Prodigal
[2023-06-28 04:59:07,472] [INFO] Running command: gunzip -c /var/lib/cwl/stg12233ea5-149c-45e3-a8ba-cf75049baab5/GCA_017941835.1_ASM1794183v1_genomic.fna.gz | prodigal -d GCA_017941835.1_ASM1794183v1_genomic.fna/cds.fna -a GCA_017941835.1_ASM1794183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:59:08,889] [INFO] Task succeeded: Prodigal
[2023-06-28 04:59:08,889] [INFO] Task started: HMMsearch
[2023-06-28 04:59:08,889] [INFO] Running command: hmmsearch --tblout GCA_017941835.1_ASM1794183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74de53e3-77ef-494f-983b-70936578aaa1/dqc_reference/reference_markers.hmm GCA_017941835.1_ASM1794183v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:59:09,148] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:59:09,149] [INFO] Found 6/6 markers.
[2023-06-28 04:59:09,167] [INFO] Query marker FASTA was written to GCA_017941835.1_ASM1794183v1_genomic.fna/markers.fasta
[2023-06-28 04:59:09,168] [INFO] Task started: Blastn
[2023-06-28 04:59:09,168] [INFO] Running command: blastn -query GCA_017941835.1_ASM1794183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74de53e3-77ef-494f-983b-70936578aaa1/dqc_reference/reference_markers.fasta -out GCA_017941835.1_ASM1794183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:09,785] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:09,789] [INFO] Selected 15 target genomes.
[2023-06-28 04:59:09,789] [INFO] Target genome list was writen to GCA_017941835.1_ASM1794183v1_genomic.fna/target_genomes.txt
[2023-06-28 04:59:09,794] [INFO] Task started: fastANI
[2023-06-28 04:59:09,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg12233ea5-149c-45e3-a8ba-cf75049baab5/GCA_017941835.1_ASM1794183v1_genomic.fna.gz --refList GCA_017941835.1_ASM1794183v1_genomic.fna/target_genomes.txt --output GCA_017941835.1_ASM1794183v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:59:16,286] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:16,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74de53e3-77ef-494f-983b-70936578aaa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:59:16,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74de53e3-77ef-494f-983b-70936578aaa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:59:16,289] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:59:16,289] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:59:16,289] [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
--------------------------------------------------------------------------------
[2023-06-28 04:59:16,290] [INFO] DFAST Taxonomy check result was written to GCA_017941835.1_ASM1794183v1_genomic.fna/tc_result.tsv
[2023-06-28 04:59:16,291] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:59:16,291] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:59:16,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74de53e3-77ef-494f-983b-70936578aaa1/dqc_reference/checkm_data
[2023-06-28 04:59:16,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:59:16,314] [INFO] Task started: CheckM
[2023-06-28 04:59:16,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017941835.1_ASM1794183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017941835.1_ASM1794183v1_genomic.fna/checkm_input GCA_017941835.1_ASM1794183v1_genomic.fna/checkm_result
[2023-06-28 04:59:30,348] [INFO] Task succeeded: CheckM
[2023-06-28 04:59:30,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.16%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 04:59:30,387] [INFO] ===== Completeness check finished =====
[2023-06-28 04:59:30,387] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:59:30,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017941835.1_ASM1794183v1_genomic.fna/markers.fasta)
[2023-06-28 04:59:30,388] [INFO] Task started: Blastn
[2023-06-28 04:59:30,388] [INFO] Running command: blastn -query GCA_017941835.1_ASM1794183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74de53e3-77ef-494f-983b-70936578aaa1/dqc_reference/reference_markers_gtdb.fasta -out GCA_017941835.1_ASM1794183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:31,270] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:31,275] [INFO] Selected 20 target genomes.
[2023-06-28 04:59:31,276] [INFO] Target genome list was writen to GCA_017941835.1_ASM1794183v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:59:31,296] [INFO] Task started: fastANI
[2023-06-28 04:59:31,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg12233ea5-149c-45e3-a8ba-cf75049baab5/GCA_017941835.1_ASM1794183v1_genomic.fna.gz --refList GCA_017941835.1_ASM1794183v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017941835.1_ASM1794183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:59:34,631] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:34,637] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:59:34,637] [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_017941835.1	s__Nanosyncoccus sp017941835	100.0	184	188	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017652765.1	s__Nanosyncoccus sp017652765	79.2818	86	188	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455145.1	s__Nanosyncoccus sp017455145	79.0791	54	188	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017404515.1	s__Nanosyncoccus sp017404515	77.7168	53	188	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	95.40	95.40	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-28 04:59:34,640] [INFO] GTDB search result was written to GCA_017941835.1_ASM1794183v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:59:34,641] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:59:34,647] [INFO] DFAST_QC result json was written to GCA_017941835.1_ASM1794183v1_genomic.fna/dqc_result.json
[2023-06-28 04:59:34,648] [INFO] DFAST_QC completed!
[2023-06-28 04:59:34,648] [INFO] Total running time: 0h0m29s