[2023-06-28 04:01:19,368] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:01:19,373] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:01:19,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgebefde5f-5d10-4e50-9155-368469b30973/dqc_reference
[2023-06-28 04:01:21,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:01:21,647] [INFO] Task started: Prodigal
[2023-06-28 04:01:21,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f6f1a77-ef17-4985-82f6-23759909b9b7/GCA_017428205.1_ASM1742820v1_genomic.fna.gz | prodigal -d GCA_017428205.1_ASM1742820v1_genomic.fna/cds.fna -a GCA_017428205.1_ASM1742820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:01:25,771] [INFO] Task succeeded: Prodigal
[2023-06-28 04:01:25,772] [INFO] Task started: HMMsearch
[2023-06-28 04:01:25,772] [INFO] Running command: hmmsearch --tblout GCA_017428205.1_ASM1742820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebefde5f-5d10-4e50-9155-368469b30973/dqc_reference/reference_markers.hmm GCA_017428205.1_ASM1742820v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:01:25,981] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:01:25,982] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4f6f1a77-ef17-4985-82f6-23759909b9b7/GCA_017428205.1_ASM1742820v1_genomic.fna.gz]
[2023-06-28 04:01:26,004] [INFO] Query marker FASTA was written to GCA_017428205.1_ASM1742820v1_genomic.fna/markers.fasta
[2023-06-28 04:01:26,004] [INFO] Task started: Blastn
[2023-06-28 04:01:26,005] [INFO] Running command: blastn -query GCA_017428205.1_ASM1742820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebefde5f-5d10-4e50-9155-368469b30973/dqc_reference/reference_markers.fasta -out GCA_017428205.1_ASM1742820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:01:26,539] [INFO] Task succeeded: Blastn
[2023-06-28 04:01:26,544] [INFO] Selected 11 target genomes.
[2023-06-28 04:01:26,544] [INFO] Target genome list was writen to GCA_017428205.1_ASM1742820v1_genomic.fna/target_genomes.txt
[2023-06-28 04:01:26,576] [INFO] Task started: fastANI
[2023-06-28 04:01:26,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f6f1a77-ef17-4985-82f6-23759909b9b7/GCA_017428205.1_ASM1742820v1_genomic.fna.gz --refList GCA_017428205.1_ASM1742820v1_genomic.fna/target_genomes.txt --output GCA_017428205.1_ASM1742820v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:01:32,794] [INFO] Task succeeded: fastANI
[2023-06-28 04:01:32,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebefde5f-5d10-4e50-9155-368469b30973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:01:32,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebefde5f-5d10-4e50-9155-368469b30973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:01:32,798] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:01:32,798] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:01:32,798] [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 04:01:32,801] [INFO] DFAST Taxonomy check result was written to GCA_017428205.1_ASM1742820v1_genomic.fna/tc_result.tsv
[2023-06-28 04:01:32,801] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:01:32,802] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:01:32,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebefde5f-5d10-4e50-9155-368469b30973/dqc_reference/checkm_data
[2023-06-28 04:01:32,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:01:32,838] [INFO] Task started: CheckM
[2023-06-28 04:01:32,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017428205.1_ASM1742820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017428205.1_ASM1742820v1_genomic.fna/checkm_input GCA_017428205.1_ASM1742820v1_genomic.fna/checkm_result
[2023-06-28 04:01:52,627] [INFO] Task succeeded: CheckM
[2023-06-28 04:01:52,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 10.30%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:01:52,652] [INFO] ===== Completeness check finished =====
[2023-06-28 04:01:52,653] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:01:52,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017428205.1_ASM1742820v1_genomic.fna/markers.fasta)
[2023-06-28 04:01:52,653] [INFO] Task started: Blastn
[2023-06-28 04:01:52,654] [INFO] Running command: blastn -query GCA_017428205.1_ASM1742820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebefde5f-5d10-4e50-9155-368469b30973/dqc_reference/reference_markers_gtdb.fasta -out GCA_017428205.1_ASM1742820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:01:53,340] [INFO] Task succeeded: Blastn
[2023-06-28 04:01:53,345] [INFO] Selected 6 target genomes.
[2023-06-28 04:01:53,345] [INFO] Target genome list was writen to GCA_017428205.1_ASM1742820v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:01:53,349] [INFO] Task started: fastANI
[2023-06-28 04:01:53,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f6f1a77-ef17-4985-82f6-23759909b9b7/GCA_017428205.1_ASM1742820v1_genomic.fna.gz --refList GCA_017428205.1_ASM1742820v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017428205.1_ASM1742820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:01:55,958] [INFO] Task succeeded: fastANI
[2023-06-28 04:01:55,968] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:01:55,968] [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_017412505.1	s__RUG11894 sp017412505	98.8993	428	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	97.05	95.90	0.86	0.80	9	conclusive
GCA_017619985.1	s__RUG11894 sp017619985	85.9508	306	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557505.1	s__RUG11894 sp017557505	85.9327	393	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773665.1	s__RUG11894 sp902773665	84.5957	365	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	97.59	96.15	0.91	0.88	4	-
GCA_017626845.1	s__RUG11894 sp017626845	84.5752	354	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:01:55,970] [INFO] GTDB search result was written to GCA_017428205.1_ASM1742820v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:01:55,971] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:01:55,976] [INFO] DFAST_QC result json was written to GCA_017428205.1_ASM1742820v1_genomic.fna/dqc_result.json
[2023-06-28 04:01:55,976] [INFO] DFAST_QC completed!
[2023-06-28 04:01:55,977] [INFO] Total running time: 0h0m37s