[2023-06-28 02:21:47,806] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:21:47,809] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:21:47,809] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2f8466d-778f-4113-b40a-2ed7fcdadf65/dqc_reference
[2023-06-28 02:21:49,231] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:21:49,235] [INFO] Task started: Prodigal
[2023-06-28 02:21:49,235] [INFO] Running command: gunzip -c /var/lib/cwl/stgee35eaec-ebd4-4462-9ba7-2f679c50cce6/GCA_944322925.1_BRZ_RL_bin66_genomic.fna.gz | prodigal -d GCA_944322925.1_BRZ_RL_bin66_genomic.fna/cds.fna -a GCA_944322925.1_BRZ_RL_bin66_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:22:00,414] [INFO] Task succeeded: Prodigal
[2023-06-28 02:22:00,414] [INFO] Task started: HMMsearch
[2023-06-28 02:22:00,414] [INFO] Running command: hmmsearch --tblout GCA_944322925.1_BRZ_RL_bin66_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2f8466d-778f-4113-b40a-2ed7fcdadf65/dqc_reference/reference_markers.hmm GCA_944322925.1_BRZ_RL_bin66_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:22:00,668] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:22:00,670] [INFO] Found 6/6 markers.
[2023-06-28 02:22:00,692] [INFO] Query marker FASTA was written to GCA_944322925.1_BRZ_RL_bin66_genomic.fna/markers.fasta
[2023-06-28 02:22:00,693] [INFO] Task started: Blastn
[2023-06-28 02:22:00,693] [INFO] Running command: blastn -query GCA_944322925.1_BRZ_RL_bin66_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2f8466d-778f-4113-b40a-2ed7fcdadf65/dqc_reference/reference_markers.fasta -out GCA_944322925.1_BRZ_RL_bin66_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:01,288] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:01,293] [INFO] Selected 30 target genomes.
[2023-06-28 02:22:01,294] [INFO] Target genome list was writen to GCA_944322925.1_BRZ_RL_bin66_genomic.fna/target_genomes.txt
[2023-06-28 02:22:01,297] [INFO] Task started: fastANI
[2023-06-28 02:22:01,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgee35eaec-ebd4-4462-9ba7-2f679c50cce6/GCA_944322925.1_BRZ_RL_bin66_genomic.fna.gz --refList GCA_944322925.1_BRZ_RL_bin66_genomic.fna/target_genomes.txt --output GCA_944322925.1_BRZ_RL_bin66_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:22:23,645] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:23,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2f8466d-778f-4113-b40a-2ed7fcdadf65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:22:23,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2f8466d-778f-4113-b40a-2ed7fcdadf65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:22:23,649] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:22:23,649] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 02:22:23,649] [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 02:22:23,651] [INFO] DFAST Taxonomy check result was written to GCA_944322925.1_BRZ_RL_bin66_genomic.fna/tc_result.tsv
[2023-06-28 02:22:23,652] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:22:23,652] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:22:23,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2f8466d-778f-4113-b40a-2ed7fcdadf65/dqc_reference/checkm_data
[2023-06-28 02:22:23,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:22:23,687] [INFO] Task started: CheckM
[2023-06-28 02:22:23,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944322925.1_BRZ_RL_bin66_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944322925.1_BRZ_RL_bin66_genomic.fna/checkm_input GCA_944322925.1_BRZ_RL_bin66_genomic.fna/checkm_result
[2023-06-28 02:22:59,990] [INFO] Task succeeded: CheckM
[2023-06-28 02:22:59,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:23:00,013] [INFO] ===== Completeness check finished =====
[2023-06-28 02:23:00,013] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:23:00,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944322925.1_BRZ_RL_bin66_genomic.fna/markers.fasta)
[2023-06-28 02:23:00,014] [INFO] Task started: Blastn
[2023-06-28 02:23:00,014] [INFO] Running command: blastn -query GCA_944322925.1_BRZ_RL_bin66_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2f8466d-778f-4113-b40a-2ed7fcdadf65/dqc_reference/reference_markers_gtdb.fasta -out GCA_944322925.1_BRZ_RL_bin66_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:23:00,809] [INFO] Task succeeded: Blastn
[2023-06-28 02:23:00,814] [INFO] Selected 25 target genomes.
[2023-06-28 02:23:00,815] [INFO] Target genome list was writen to GCA_944322925.1_BRZ_RL_bin66_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:23:00,821] [INFO] Task started: fastANI
[2023-06-28 02:23:00,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgee35eaec-ebd4-4462-9ba7-2f679c50cce6/GCA_944322925.1_BRZ_RL_bin66_genomic.fna.gz --refList GCA_944322925.1_BRZ_RL_bin66_genomic.fna/target_genomes_gtdb.txt --output GCA_944322925.1_BRZ_RL_bin66_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:23:09,843] [INFO] Task succeeded: fastANI
[2023-06-28 02:23:09,858] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:23:09,858] [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_018711225.1	s__Cryptobacteroides intestinipullorum	78.1563	242	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694655.1	s__Cryptobacteroides merdigallinarum	77.6964	194	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694845.1	s__Cryptobacteroides intestinavium	77.4845	99	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695065.1	s__Cryptobacteroides excrementipullorum	77.425	105	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695015.1	s__Cryptobacteroides faecigallinarum	77.2455	109	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694835.1	s__Cryptobacteroides gallistercoris	77.0495	101	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060405.1	s__Cryptobacteroides sp015060405	77.0191	51	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694755.1	s__Cryptobacteroides merdavium	76.96	131	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760425.1	s__Cryptobacteroides sp900760425	76.9482	80	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695115.1	s__Cryptobacteroides avicola	76.9083	111	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694995.1	s__Cryptobacteroides faecavium	76.8309	87	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399865.1	s__Cryptobacteroides sp017399865	76.3867	53	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626355.1	s__Cryptobacteroides sp017626355	76.3736	52	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437125.1	s__Cryptobacteroides sp017437125	76.2374	56	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399905.1	s__Cryptobacteroides sp017399905	75.7077	52	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.58	97.58	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-06-28 02:23:09,860] [INFO] GTDB search result was written to GCA_944322925.1_BRZ_RL_bin66_genomic.fna/result_gtdb.tsv
[2023-06-28 02:23:09,861] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:23:09,865] [INFO] DFAST_QC result json was written to GCA_944322925.1_BRZ_RL_bin66_genomic.fna/dqc_result.json
[2023-06-28 02:23:09,865] [INFO] DFAST_QC completed!
[2023-06-28 02:23:09,865] [INFO] Total running time: 0h1m22s