[2023-06-27 23:46:08,099] [INFO] DFAST_QC pipeline started.
[2023-06-27 23:46:08,102] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 23:46:08,102] [INFO] DQC Reference Directory: /var/lib/cwl/stgdca5e8fb-e2bb-4cc2-9d7d-b52f7834d0d5/dqc_reference
[2023-06-27 23:46:09,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 23:46:09,354] [INFO] Task started: Prodigal
[2023-06-27 23:46:09,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg892ffeaa-78af-4ba4-98c8-19044382480f/GCA_026914085.1_ASM2691408v1_genomic.fna.gz | prodigal -d GCA_026914085.1_ASM2691408v1_genomic.fna/cds.fna -a GCA_026914085.1_ASM2691408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 23:46:21,822] [INFO] Task succeeded: Prodigal
[2023-06-27 23:46:21,823] [INFO] Task started: HMMsearch
[2023-06-27 23:46:21,823] [INFO] Running command: hmmsearch --tblout GCA_026914085.1_ASM2691408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdca5e8fb-e2bb-4cc2-9d7d-b52f7834d0d5/dqc_reference/reference_markers.hmm GCA_026914085.1_ASM2691408v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 23:46:22,135] [INFO] Task succeeded: HMMsearch
[2023-06-27 23:46:22,136] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg892ffeaa-78af-4ba4-98c8-19044382480f/GCA_026914085.1_ASM2691408v1_genomic.fna.gz]
[2023-06-27 23:46:22,188] [INFO] Query marker FASTA was written to GCA_026914085.1_ASM2691408v1_genomic.fna/markers.fasta
[2023-06-27 23:46:22,188] [INFO] Task started: Blastn
[2023-06-27 23:46:22,188] [INFO] Running command: blastn -query GCA_026914085.1_ASM2691408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca5e8fb-e2bb-4cc2-9d7d-b52f7834d0d5/dqc_reference/reference_markers.fasta -out GCA_026914085.1_ASM2691408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:46:22,761] [INFO] Task succeeded: Blastn
[2023-06-27 23:46:22,766] [INFO] Selected 10 target genomes.
[2023-06-27 23:46:22,767] [INFO] Target genome list was writen to GCA_026914085.1_ASM2691408v1_genomic.fna/target_genomes.txt
[2023-06-27 23:46:22,768] [INFO] Task started: fastANI
[2023-06-27 23:46:22,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg892ffeaa-78af-4ba4-98c8-19044382480f/GCA_026914085.1_ASM2691408v1_genomic.fna.gz --refList GCA_026914085.1_ASM2691408v1_genomic.fna/target_genomes.txt --output GCA_026914085.1_ASM2691408v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 23:46:30,447] [INFO] Task succeeded: fastANI
[2023-06-27 23:46:30,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdca5e8fb-e2bb-4cc2-9d7d-b52f7834d0d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 23:46:30,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdca5e8fb-e2bb-4cc2-9d7d-b52f7834d0d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 23:46:30,449] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 23:46:30,450] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 23:46:30,450] [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
--------------------------------------------------------------------------------
[2023-06-27 23:46:30,452] [INFO] DFAST Taxonomy check result was written to GCA_026914085.1_ASM2691408v1_genomic.fna/tc_result.tsv
[2023-06-27 23:46:30,453] [INFO] ===== Taxonomy check completed =====
[2023-06-27 23:46:30,453] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 23:46:30,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdca5e8fb-e2bb-4cc2-9d7d-b52f7834d0d5/dqc_reference/checkm_data
[2023-06-27 23:46:30,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 23:46:30,511] [INFO] Task started: CheckM
[2023-06-27 23:46:30,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026914085.1_ASM2691408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026914085.1_ASM2691408v1_genomic.fna/checkm_input GCA_026914085.1_ASM2691408v1_genomic.fna/checkm_result
[2023-06-27 23:47:10,461] [INFO] Task succeeded: CheckM
[2023-06-27 23:47:10,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.25%
Contamintation: 10.19%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 23:47:10,492] [INFO] ===== Completeness check finished =====
[2023-06-27 23:47:10,492] [INFO] ===== Start GTDB Search =====
[2023-06-27 23:47:10,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026914085.1_ASM2691408v1_genomic.fna/markers.fasta)
[2023-06-27 23:47:10,493] [INFO] Task started: Blastn
[2023-06-27 23:47:10,493] [INFO] Running command: blastn -query GCA_026914085.1_ASM2691408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca5e8fb-e2bb-4cc2-9d7d-b52f7834d0d5/dqc_reference/reference_markers_gtdb.fasta -out GCA_026914085.1_ASM2691408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:47:11,274] [INFO] Task succeeded: Blastn
[2023-06-27 23:47:11,279] [INFO] Selected 12 target genomes.
[2023-06-27 23:47:11,279] [INFO] Target genome list was writen to GCA_026914085.1_ASM2691408v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 23:47:11,292] [INFO] Task started: fastANI
[2023-06-27 23:47:11,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg892ffeaa-78af-4ba4-98c8-19044382480f/GCA_026914085.1_ASM2691408v1_genomic.fna.gz --refList GCA_026914085.1_ASM2691408v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026914085.1_ASM2691408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 23:47:22,903] [INFO] Task succeeded: fastANI
[2023-06-27 23:47:22,912] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 23:47:22,912] [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_009840225.1	s__Bin5 sp009840225	94.8475	1104	1379	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	97.63	95.35	0.89	0.84	3	-
GCA_011523365.1	s__Bin5 sp011523365	92.0304	1086	1379	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841235.1	s__Bin5 sp009841235	84.3879	928	1379	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	95.53	95.53	0.91	0.91	2	-
GCA_009838625.1	s__Bin5 sp009838625	83.6984	897	1379	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	99.90	99.90	0.97	0.97	2	-
GCA_002238445.1	s__Bin5 sp002238445	81.3462	772	1379	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124945.1	s__RI-153 sp016124945	75.8131	88	1379	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__RI-153	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 23:47:22,914] [INFO] GTDB search result was written to GCA_026914085.1_ASM2691408v1_genomic.fna/result_gtdb.tsv
[2023-06-27 23:47:22,915] [INFO] ===== GTDB Search completed =====
[2023-06-27 23:47:22,917] [INFO] DFAST_QC result json was written to GCA_026914085.1_ASM2691408v1_genomic.fna/dqc_result.json
[2023-06-27 23:47:22,918] [INFO] DFAST_QC completed!
[2023-06-27 23:47:22,918] [INFO] Total running time: 0h1m15s