[2023-06-08 11:32:41,598] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:32:41,601] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:32:41,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3c505bf-cd61-42d8-a454-571acc005881/dqc_reference
[2023-06-08 11:32:42,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:32:42,909] [INFO] Task started: Prodigal
[2023-06-08 11:32:42,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbdffe49-922a-4d67-a26c-d3ef7a953f9e/GCA_902635075.1_AG-439-P01_genomic.fna.gz | prodigal -d GCA_902635075.1_AG-439-P01_genomic.fna/cds.fna -a GCA_902635075.1_AG-439-P01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:32:45,596] [INFO] Task succeeded: Prodigal
[2023-06-08 11:32:45,596] [INFO] Task started: HMMsearch
[2023-06-08 11:32:45,597] [INFO] Running command: hmmsearch --tblout GCA_902635075.1_AG-439-P01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3c505bf-cd61-42d8-a454-571acc005881/dqc_reference/reference_markers.hmm GCA_902635075.1_AG-439-P01_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:32:45,807] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:32:45,808] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcbdffe49-922a-4d67-a26c-d3ef7a953f9e/GCA_902635075.1_AG-439-P01_genomic.fna.gz]
[2023-06-08 11:32:45,823] [INFO] Query marker FASTA was written to GCA_902635075.1_AG-439-P01_genomic.fna/markers.fasta
[2023-06-08 11:32:45,824] [INFO] Task started: Blastn
[2023-06-08 11:32:45,824] [INFO] Running command: blastn -query GCA_902635075.1_AG-439-P01_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3c505bf-cd61-42d8-a454-571acc005881/dqc_reference/reference_markers.fasta -out GCA_902635075.1_AG-439-P01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:32:46,373] [INFO] Task succeeded: Blastn
[2023-06-08 11:32:46,376] [INFO] Selected 9 target genomes.
[2023-06-08 11:32:46,377] [INFO] Target genome list was writen to GCA_902635075.1_AG-439-P01_genomic.fna/target_genomes.txt
[2023-06-08 11:32:46,378] [INFO] Task started: fastANI
[2023-06-08 11:32:46,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbdffe49-922a-4d67-a26c-d3ef7a953f9e/GCA_902635075.1_AG-439-P01_genomic.fna.gz --refList GCA_902635075.1_AG-439-P01_genomic.fna/target_genomes.txt --output GCA_902635075.1_AG-439-P01_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:32:49,727] [INFO] Task succeeded: fastANI
[2023-06-08 11:32:49,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3c505bf-cd61-42d8-a454-571acc005881/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:32:49,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3c505bf-cd61-42d8-a454-571acc005881/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:32:49,730] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:32:49,730] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:32:49,730] [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 11:32:49,732] [INFO] DFAST Taxonomy check result was written to GCA_902635075.1_AG-439-P01_genomic.fna/tc_result.tsv
[2023-06-08 11:32:49,732] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:32:49,732] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:32:49,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3c505bf-cd61-42d8-a454-571acc005881/dqc_reference/checkm_data
[2023-06-08 11:32:49,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:32:49,748] [INFO] Task started: CheckM
[2023-06-08 11:32:49,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902635075.1_AG-439-P01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902635075.1_AG-439-P01_genomic.fna/checkm_input GCA_902635075.1_AG-439-P01_genomic.fna/checkm_result
[2023-06-08 11:33:05,776] [INFO] Task succeeded: CheckM
[2023-06-08 11:33:05,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:33:05,795] [INFO] ===== Completeness check finished =====
[2023-06-08 11:33:05,795] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:33:05,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902635075.1_AG-439-P01_genomic.fna/markers.fasta)
[2023-06-08 11:33:05,796] [INFO] Task started: Blastn
[2023-06-08 11:33:05,796] [INFO] Running command: blastn -query GCA_902635075.1_AG-439-P01_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3c505bf-cd61-42d8-a454-571acc005881/dqc_reference/reference_markers_gtdb.fasta -out GCA_902635075.1_AG-439-P01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:33:06,600] [INFO] Task succeeded: Blastn
[2023-06-08 11:33:06,604] [INFO] Selected 13 target genomes.
[2023-06-08 11:33:06,605] [INFO] Target genome list was writen to GCA_902635075.1_AG-439-P01_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:33:06,609] [INFO] Task started: fastANI
[2023-06-08 11:33:06,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbdffe49-922a-4d67-a26c-d3ef7a953f9e/GCA_902635075.1_AG-439-P01_genomic.fna.gz --refList GCA_902635075.1_AG-439-P01_genomic.fna/target_genomes_gtdb.txt --output GCA_902635075.1_AG-439-P01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:33:09,272] [INFO] Task succeeded: fastANI
[2023-06-08 11:33:09,288] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:33:09,288] [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
GCF_001179945.1	s__Pelagibacter_A ubique_A	98.0928	146	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	98.31	98.12	0.75	0.72	3	conclusive
GCA_902597175.1	s__Pelagibacter_A sp902597175	89.149	240	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635225.1	s__Pelagibacter_A sp902635225	89.0782	167	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	99.75	99.75	0.71	0.71	2	-
GCA_902585045.1	s__Pelagibacter_A sp902585045	89.0242	217	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	99.73	99.73	0.82	0.82	2	-
GCA_902535505.1	s__Pelagibacter_A sp902535505	88.4185	169	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557605.1	s__Pelagibacter_A sp902557605	85.4316	124	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616145.1	s__Pelagibacter_A sp902616145	84.5837	205	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557775.1	s__Pelagibacter_A sp902557775	84.359	184	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902598735.1	s__Pelagibacter_A sp902598735	83.9618	179	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595375.1	s__Pelagibacter_A sp902595375	83.7357	164	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556855.1	s__Pelagibacter_A sp902556855	82.9106	149	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902545945.1	s__Pelagibacter_A sp902545945	81.6971	135	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536305.1	s__Pelagibacter_A sp902536305	79.1886	135	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:33:09,292] [INFO] GTDB search result was written to GCA_902635075.1_AG-439-P01_genomic.fna/result_gtdb.tsv
[2023-06-08 11:33:09,293] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:33:09,296] [INFO] DFAST_QC result json was written to GCA_902635075.1_AG-439-P01_genomic.fna/dqc_result.json
[2023-06-08 11:33:09,296] [INFO] DFAST_QC completed!
[2023-06-08 11:33:09,296] [INFO] Total running time: 0h0m28s