[2023-06-08 09:05:11,935] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:05:11,937] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:05:11,938] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1543cf9-73b2-4826-b476-bd91f6c6da97/dqc_reference
[2023-06-08 09:05:13,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:05:13,437] [INFO] Task started: Prodigal
[2023-06-08 09:05:13,438] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa283639-edf5-4c18-bed5-530ca0ed3d67/GCA_902614745.1_AG-919-C14_genomic.fna.gz | prodigal -d GCA_902614745.1_AG-919-C14_genomic.fna/cds.fna -a GCA_902614745.1_AG-919-C14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:05:15,841] [INFO] Task succeeded: Prodigal
[2023-06-08 09:05:15,841] [INFO] Task started: HMMsearch
[2023-06-08 09:05:15,842] [INFO] Running command: hmmsearch --tblout GCA_902614745.1_AG-919-C14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1543cf9-73b2-4826-b476-bd91f6c6da97/dqc_reference/reference_markers.hmm GCA_902614745.1_AG-919-C14_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:05:15,959] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:05:15,961] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgfa283639-edf5-4c18-bed5-530ca0ed3d67/GCA_902614745.1_AG-919-C14_genomic.fna.gz]
[2023-06-08 09:05:15,996] [INFO] Query marker FASTA was written to GCA_902614745.1_AG-919-C14_genomic.fna/markers.fasta
[2023-06-08 09:05:15,997] [INFO] Task started: Blastn
[2023-06-08 09:05:15,997] [INFO] Running command: blastn -query GCA_902614745.1_AG-919-C14_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1543cf9-73b2-4826-b476-bd91f6c6da97/dqc_reference/reference_markers.fasta -out GCA_902614745.1_AG-919-C14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:16,490] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:16,493] [INFO] Selected 5 target genomes.
[2023-06-08 09:05:16,494] [INFO] Target genome list was writen to GCA_902614745.1_AG-919-C14_genomic.fna/target_genomes.txt
[2023-06-08 09:05:16,494] [INFO] Task started: fastANI
[2023-06-08 09:05:16,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa283639-edf5-4c18-bed5-530ca0ed3d67/GCA_902614745.1_AG-919-C14_genomic.fna.gz --refList GCA_902614745.1_AG-919-C14_genomic.fna/target_genomes.txt --output GCA_902614745.1_AG-919-C14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:05:19,418] [INFO] Task succeeded: fastANI
[2023-06-08 09:05:19,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1543cf9-73b2-4826-b476-bd91f6c6da97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:05:19,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1543cf9-73b2-4826-b476-bd91f6c6da97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:05:19,421] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:05:19,421] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:05:19,422] [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
--------------------------------------------------------------------------------
[2023-06-08 09:05:19,424] [INFO] DFAST Taxonomy check result was written to GCA_902614745.1_AG-919-C14_genomic.fna/tc_result.tsv
[2023-06-08 09:05:19,425] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:05:19,425] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:05:19,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1543cf9-73b2-4826-b476-bd91f6c6da97/dqc_reference/checkm_data
[2023-06-08 09:05:19,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:05:19,437] [INFO] Task started: CheckM
[2023-06-08 09:05:19,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614745.1_AG-919-C14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614745.1_AG-919-C14_genomic.fna/checkm_input GCA_902614745.1_AG-919-C14_genomic.fna/checkm_result
[2023-06-08 09:05:34,336] [INFO] Task succeeded: CheckM
[2023-06-08 09:05:34,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:05:34,354] [INFO] ===== Completeness check finished =====
[2023-06-08 09:05:34,354] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:05:34,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614745.1_AG-919-C14_genomic.fna/markers.fasta)
[2023-06-08 09:05:34,355] [INFO] Task started: Blastn
[2023-06-08 09:05:34,355] [INFO] Running command: blastn -query GCA_902614745.1_AG-919-C14_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1543cf9-73b2-4826-b476-bd91f6c6da97/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614745.1_AG-919-C14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:34,832] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:34,836] [INFO] Selected 5 target genomes.
[2023-06-08 09:05:34,837] [INFO] Target genome list was writen to GCA_902614745.1_AG-919-C14_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:05:34,838] [INFO] Task started: fastANI
[2023-06-08 09:05:34,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa283639-edf5-4c18-bed5-530ca0ed3d67/GCA_902614745.1_AG-919-C14_genomic.fna.gz --refList GCA_902614745.1_AG-919-C14_genomic.fna/target_genomes_gtdb.txt --output GCA_902614745.1_AG-919-C14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:05:36,065] [INFO] Task succeeded: fastANI
[2023-06-08 09:05:36,071] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:05:36,071] [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_002862705.1	s__UBA7446 sp002862705	98.2846	133	147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	conclusive
GCA_002313325.1	s__UBA7446 sp002313325	91.9892	80	147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.90	99.90	0.92	0.92	2	-
GCA_009886265.1	s__UBA7446 sp009886265	91.3361	107	147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698745.1	s__UBA7446 sp002698745	84.3058	101	147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862645.1	s__UBA7446 sp002862645	83.9872	100	147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-06-08 09:05:36,073] [INFO] GTDB search result was written to GCA_902614745.1_AG-919-C14_genomic.fna/result_gtdb.tsv
[2023-06-08 09:05:36,074] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:05:36,076] [INFO] DFAST_QC result json was written to GCA_902614745.1_AG-919-C14_genomic.fna/dqc_result.json
[2023-06-08 09:05:36,076] [INFO] DFAST_QC completed!
[2023-06-08 09:05:36,076] [INFO] Total running time: 0h0m24s