[2023-06-13 21:20:32,352] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:32,355] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:32,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg92c3f3ba-c142-4671-baa6-a1d53f9c76a4/dqc_reference
[2023-06-13 21:20:33,498] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:33,499] [INFO] Task started: Prodigal
[2023-06-13 21:20:33,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg83238de6-1900-4064-b19b-3b74e420f5b3/GCA_947259255.1_ERZ12284667_genomic.fna.gz | prodigal -d GCA_947259255.1_ERZ12284667_genomic.fna/cds.fna -a GCA_947259255.1_ERZ12284667_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:38,524] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:38,524] [INFO] Task started: HMMsearch
[2023-06-13 21:20:38,524] [INFO] Running command: hmmsearch --tblout GCA_947259255.1_ERZ12284667_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92c3f3ba-c142-4671-baa6-a1d53f9c76a4/dqc_reference/reference_markers.hmm GCA_947259255.1_ERZ12284667_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:38,750] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:38,751] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg83238de6-1900-4064-b19b-3b74e420f5b3/GCA_947259255.1_ERZ12284667_genomic.fna.gz]
[2023-06-13 21:20:38,772] [INFO] Query marker FASTA was written to GCA_947259255.1_ERZ12284667_genomic.fna/markers.fasta
[2023-06-13 21:20:38,772] [INFO] Task started: Blastn
[2023-06-13 21:20:38,772] [INFO] Running command: blastn -query GCA_947259255.1_ERZ12284667_genomic.fna/markers.fasta -db /var/lib/cwl/stg92c3f3ba-c142-4671-baa6-a1d53f9c76a4/dqc_reference/reference_markers.fasta -out GCA_947259255.1_ERZ12284667_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:39,401] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:39,405] [INFO] Selected 30 target genomes.
[2023-06-13 21:20:39,405] [INFO] Target genome list was writen to GCA_947259255.1_ERZ12284667_genomic.fna/target_genomes.txt
[2023-06-13 21:20:39,408] [INFO] Task started: fastANI
[2023-06-13 21:20:39,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg83238de6-1900-4064-b19b-3b74e420f5b3/GCA_947259255.1_ERZ12284667_genomic.fna.gz --refList GCA_947259255.1_ERZ12284667_genomic.fna/target_genomes.txt --output GCA_947259255.1_ERZ12284667_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:20:59,636] [INFO] Task succeeded: fastANI
[2023-06-13 21:20:59,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92c3f3ba-c142-4671-baa6-a1d53f9c76a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:20:59,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92c3f3ba-c142-4671-baa6-a1d53f9c76a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:20:59,638] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:20:59,638] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 21:20:59,638] [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
--------------------------------------------------------------------------------
[2023-06-13 21:20:59,640] [INFO] DFAST Taxonomy check result was written to GCA_947259255.1_ERZ12284667_genomic.fna/tc_result.tsv
[2023-06-13 21:20:59,640] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:20:59,640] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:20:59,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92c3f3ba-c142-4671-baa6-a1d53f9c76a4/dqc_reference/checkm_data
[2023-06-13 21:20:59,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:20:59,673] [INFO] Task started: CheckM
[2023-06-13 21:20:59,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947259255.1_ERZ12284667_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947259255.1_ERZ12284667_genomic.fna/checkm_input GCA_947259255.1_ERZ12284667_genomic.fna/checkm_result
[2023-06-13 21:21:19,223] [INFO] Task succeeded: CheckM
[2023-06-13 21:21:19,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.59%
Contamintation: 3.36%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-06-13 21:21:19,239] [INFO] ===== Completeness check finished =====
[2023-06-13 21:21:19,239] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:21:19,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947259255.1_ERZ12284667_genomic.fna/markers.fasta)
[2023-06-13 21:21:19,240] [INFO] Task started: Blastn
[2023-06-13 21:21:19,240] [INFO] Running command: blastn -query GCA_947259255.1_ERZ12284667_genomic.fna/markers.fasta -db /var/lib/cwl/stg92c3f3ba-c142-4671-baa6-a1d53f9c76a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_947259255.1_ERZ12284667_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:20,215] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:20,218] [INFO] Selected 20 target genomes.
[2023-06-13 21:21:20,219] [INFO] Target genome list was writen to GCA_947259255.1_ERZ12284667_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:21:20,283] [INFO] Task started: fastANI
[2023-06-13 21:21:20,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg83238de6-1900-4064-b19b-3b74e420f5b3/GCA_947259255.1_ERZ12284667_genomic.fna.gz --refList GCA_947259255.1_ERZ12284667_genomic.fna/target_genomes_gtdb.txt --output GCA_947259255.1_ERZ12284667_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:21:29,336] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:29,343] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:21:29,343] [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_013042375.1	s__UBA1847 sp013042375	77.9893	165	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_004282875.1	s__UBA1847 sp004282875	77.7777	138	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043165.1	s__UBA1847 sp013043165	77.7042	161	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_013001045.1	s__UBA1847 sp013001045	77.5501	131	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.51	99.51	0.75	0.75	2	-
GCA_009937605.1	s__UBA1847 sp009937605	77.4448	113	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937525.1	s__JAACFE01 sp009937525	77.1218	104	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011772865.1	s__JAACFB01 sp011772865	76.9847	108	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	99.97	99.97	0.99	0.99	3	-
GCA_009937615.1	s__JAACFB01 sp009937615	76.8375	99	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138675.1	s__JAACFB01 sp013138675	76.7158	72	496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:21:29,345] [INFO] GTDB search result was written to GCA_947259255.1_ERZ12284667_genomic.fna/result_gtdb.tsv
[2023-06-13 21:21:29,345] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:21:29,348] [INFO] DFAST_QC result json was written to GCA_947259255.1_ERZ12284667_genomic.fna/dqc_result.json
[2023-06-13 21:21:29,348] [INFO] DFAST_QC completed!
[2023-06-13 21:21:29,348] [INFO] Total running time: 0h0m57s