[2023-06-08 17:47:34,351] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:47:34,353] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:47:34,354] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa73a0d4-7da3-41f1-b6fa-e2b9f6058758/dqc_reference
[2023-06-08 17:47:35,774] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:47:35,775] [INFO] Task started: Prodigal
[2023-06-08 17:47:35,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c466360-ed28-4ab1-91e1-83a49b60256c/GCA_902634985.1_AG-439-O12_genomic.fna.gz | prodigal -d GCA_902634985.1_AG-439-O12_genomic.fna/cds.fna -a GCA_902634985.1_AG-439-O12_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:47:38,014] [INFO] Task succeeded: Prodigal
[2023-06-08 17:47:38,015] [INFO] Task started: HMMsearch
[2023-06-08 17:47:38,015] [INFO] Running command: hmmsearch --tblout GCA_902634985.1_AG-439-O12_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa73a0d4-7da3-41f1-b6fa-e2b9f6058758/dqc_reference/reference_markers.hmm GCA_902634985.1_AG-439-O12_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:47:38,174] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:47:38,176] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8c466360-ed28-4ab1-91e1-83a49b60256c/GCA_902634985.1_AG-439-O12_genomic.fna.gz]
[2023-06-08 17:47:38,192] [INFO] Query marker FASTA was written to GCA_902634985.1_AG-439-O12_genomic.fna/markers.fasta
[2023-06-08 17:47:38,192] [INFO] Task started: Blastn
[2023-06-08 17:47:38,192] [INFO] Running command: blastn -query GCA_902634985.1_AG-439-O12_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa73a0d4-7da3-41f1-b6fa-e2b9f6058758/dqc_reference/reference_markers.fasta -out GCA_902634985.1_AG-439-O12_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:47:38,795] [INFO] Task succeeded: Blastn
[2023-06-08 17:47:38,799] [INFO] Selected 11 target genomes.
[2023-06-08 17:47:38,799] [INFO] Target genome list was writen to GCA_902634985.1_AG-439-O12_genomic.fna/target_genomes.txt
[2023-06-08 17:47:38,801] [INFO] Task started: fastANI
[2023-06-08 17:47:38,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c466360-ed28-4ab1-91e1-83a49b60256c/GCA_902634985.1_AG-439-O12_genomic.fna.gz --refList GCA_902634985.1_AG-439-O12_genomic.fna/target_genomes.txt --output GCA_902634985.1_AG-439-O12_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:47:43,382] [INFO] Task succeeded: fastANI
[2023-06-08 17:47:43,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa73a0d4-7da3-41f1-b6fa-e2b9f6058758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:47:43,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa73a0d4-7da3-41f1-b6fa-e2b9f6058758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:47:43,386] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:47:43,386] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:47:43,386] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	76.7594	52	240	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:47:43,389] [INFO] DFAST Taxonomy check result was written to GCA_902634985.1_AG-439-O12_genomic.fna/tc_result.tsv
[2023-06-08 17:47:43,389] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:47:43,389] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:47:43,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa73a0d4-7da3-41f1-b6fa-e2b9f6058758/dqc_reference/checkm_data
[2023-06-08 17:47:43,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:47:43,405] [INFO] Task started: CheckM
[2023-06-08 17:47:43,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902634985.1_AG-439-O12_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902634985.1_AG-439-O12_genomic.fna/checkm_input GCA_902634985.1_AG-439-O12_genomic.fna/checkm_result
[2023-06-08 17:47:58,377] [INFO] Task succeeded: CheckM
[2023-06-08 17:47:58,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:47:58,396] [INFO] ===== Completeness check finished =====
[2023-06-08 17:47:58,396] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:47:58,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902634985.1_AG-439-O12_genomic.fna/markers.fasta)
[2023-06-08 17:47:58,397] [INFO] Task started: Blastn
[2023-06-08 17:47:58,397] [INFO] Running command: blastn -query GCA_902634985.1_AG-439-O12_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa73a0d4-7da3-41f1-b6fa-e2b9f6058758/dqc_reference/reference_markers_gtdb.fasta -out GCA_902634985.1_AG-439-O12_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:47:58,874] [INFO] Task succeeded: Blastn
[2023-06-08 17:47:58,878] [INFO] Selected 15 target genomes.
[2023-06-08 17:47:58,878] [INFO] Target genome list was writen to GCA_902634985.1_AG-439-O12_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:47:58,885] [INFO] Task started: fastANI
[2023-06-08 17:47:58,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c466360-ed28-4ab1-91e1-83a49b60256c/GCA_902634985.1_AG-439-O12_genomic.fna.gz --refList GCA_902634985.1_AG-439-O12_genomic.fna/target_genomes_gtdb.txt --output GCA_902634985.1_AG-439-O12_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:48:01,770] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:01,785] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 17:48:01,785] [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_902561465.1	s__AG-414-E02 sp902561465	83.2728	111	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607525.1	s__AG-414-E02 sp902607525	82.8909	103	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608065.1	s__AG-414-E02 sp902608065	82.3906	92	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607735.1	s__AG-414-E02 sp902607735	82.2409	97	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588335.1	s__AG-414-E02 sp902588335	81.9224	94	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607585.1	s__AG-414-E02 sp902607585	81.7896	91	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902567785.1	s__AG-414-E02 sp902567785	81.7604	115	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607625.1	s__AG-414-E02 sp902607625	81.1258	121	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519445.1	s__AG-414-E02 sp902519445	81.1066	92	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589795.1	s__AG-414-E02 sp902589795	80.5355	88	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213215.1	s__AG-414-E02 sp004213215	79.5033	134	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000299095.1	s__Pelagibacter sp000299095	76.4453	59	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:48:01,787] [INFO] GTDB search result was written to GCA_902634985.1_AG-439-O12_genomic.fna/result_gtdb.tsv
[2023-06-08 17:48:01,788] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:48:01,791] [INFO] DFAST_QC result json was written to GCA_902634985.1_AG-439-O12_genomic.fna/dqc_result.json
[2023-06-08 17:48:01,791] [INFO] DFAST_QC completed!
[2023-06-08 17:48:01,792] [INFO] Total running time: 0h0m27s