[2023-06-28 19:48:37,988] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:37,991] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:37,991] [INFO] DQC Reference Directory: /var/lib/cwl/stg910dbd53-7c90-4b51-a04c-0f15e200e0b8/dqc_reference
[2023-06-28 19:48:39,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:39,307] [INFO] Task started: Prodigal
[2023-06-28 19:48:39,308] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f863385-4c7a-4e23-bd7c-1b67b1981a9d/GCA_017482785.1_ASM1748278v1_genomic.fna.gz | prodigal -d GCA_017482785.1_ASM1748278v1_genomic.fna/cds.fna -a GCA_017482785.1_ASM1748278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:41,180] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:41,181] [INFO] Task started: HMMsearch
[2023-06-28 19:48:41,181] [INFO] Running command: hmmsearch --tblout GCA_017482785.1_ASM1748278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg910dbd53-7c90-4b51-a04c-0f15e200e0b8/dqc_reference/reference_markers.hmm GCA_017482785.1_ASM1748278v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:41,401] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:41,403] [INFO] Found 6/6 markers.
[2023-06-28 19:48:41,416] [INFO] Query marker FASTA was written to GCA_017482785.1_ASM1748278v1_genomic.fna/markers.fasta
[2023-06-28 19:48:41,417] [INFO] Task started: Blastn
[2023-06-28 19:48:41,417] [INFO] Running command: blastn -query GCA_017482785.1_ASM1748278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg910dbd53-7c90-4b51-a04c-0f15e200e0b8/dqc_reference/reference_markers.fasta -out GCA_017482785.1_ASM1748278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:42,433] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:42,437] [INFO] Selected 13 target genomes.
[2023-06-28 19:48:42,438] [INFO] Target genome list was writen to GCA_017482785.1_ASM1748278v1_genomic.fna/target_genomes.txt
[2023-06-28 19:48:42,573] [INFO] Task started: fastANI
[2023-06-28 19:48:42,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f863385-4c7a-4e23-bd7c-1b67b1981a9d/GCA_017482785.1_ASM1748278v1_genomic.fna.gz --refList GCA_017482785.1_ASM1748278v1_genomic.fna/target_genomes.txt --output GCA_017482785.1_ASM1748278v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:52,530] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:52,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg910dbd53-7c90-4b51-a04c-0f15e200e0b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:52,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg910dbd53-7c90-4b51-a04c-0f15e200e0b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:52,533] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:52,534] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:48:52,534] [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 19:48:52,536] [INFO] DFAST Taxonomy check result was written to GCA_017482785.1_ASM1748278v1_genomic.fna/tc_result.tsv
[2023-06-28 19:48:52,537] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:52,538] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:52,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg910dbd53-7c90-4b51-a04c-0f15e200e0b8/dqc_reference/checkm_data
[2023-06-28 19:48:52,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:52,556] [INFO] Task started: CheckM
[2023-06-28 19:48:52,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017482785.1_ASM1748278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017482785.1_ASM1748278v1_genomic.fna/checkm_input GCA_017482785.1_ASM1748278v1_genomic.fna/checkm_result
[2023-06-28 19:49:06,905] [INFO] Task succeeded: CheckM
[2023-06-28 19:49:06,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:49:06,925] [INFO] ===== Completeness check finished =====
[2023-06-28 19:49:06,925] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:49:06,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017482785.1_ASM1748278v1_genomic.fna/markers.fasta)
[2023-06-28 19:49:06,926] [INFO] Task started: Blastn
[2023-06-28 19:49:06,926] [INFO] Running command: blastn -query GCA_017482785.1_ASM1748278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg910dbd53-7c90-4b51-a04c-0f15e200e0b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_017482785.1_ASM1748278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:07,730] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:07,733] [INFO] Selected 17 target genomes.
[2023-06-28 19:49:07,734] [INFO] Target genome list was writen to GCA_017482785.1_ASM1748278v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:49:07,766] [INFO] Task started: fastANI
[2023-06-28 19:49:07,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f863385-4c7a-4e23-bd7c-1b67b1981a9d/GCA_017482785.1_ASM1748278v1_genomic.fna.gz --refList GCA_017482785.1_ASM1748278v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017482785.1_ASM1748278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:49:10,609] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:10,615] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:49:10,615] [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_017406405.1	s__Nanosyncoccus sp017406405	78.4297	81	264	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432365.1	s__Nanosyncoccus sp017432365	78.0198	71	264	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017515285.1	s__Nanosyncoccus sp017515285	78.0183	77	264	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545595.1	s__Nanosyncoccus sp017545595	77.8274	78	264	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432425.1	s__Nanosyncoccus sp017432425	77.1085	72	264	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:49:10,618] [INFO] GTDB search result was written to GCA_017482785.1_ASM1748278v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:49:10,618] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:49:10,621] [INFO] DFAST_QC result json was written to GCA_017482785.1_ASM1748278v1_genomic.fna/dqc_result.json
[2023-06-28 19:49:10,621] [INFO] DFAST_QC completed!
[2023-06-28 19:49:10,621] [INFO] Total running time: 0h0m33s