[2023-03-15 15:06:33,786] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:06:33,788] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:06:33,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg232f2b89-c2dd-4a59-94d3-9abcc6777134/dqc_reference
[2023-03-15 15:06:34,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:06:34,864] [INFO] Task started: Prodigal
[2023-03-15 15:06:34,864] [INFO] Running command: cat /var/lib/cwl/stg583bf0a3-9aae-4943-9987-c7f1802476ee/OceanDNA-b31316.fa | prodigal -d OceanDNA-b31316/cds.fna -a OceanDNA-b31316/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:06:37,594] [INFO] Task succeeded: Prodigal
[2023-03-15 15:06:37,594] [INFO] Task started: HMMsearch
[2023-03-15 15:06:37,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b31316/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg232f2b89-c2dd-4a59-94d3-9abcc6777134/dqc_reference/reference_markers.hmm OceanDNA-b31316/protein.faa > /dev/null
[2023-03-15 15:06:37,741] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:06:37,742] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg583bf0a3-9aae-4943-9987-c7f1802476ee/OceanDNA-b31316.fa]
[2023-03-15 15:06:37,782] [INFO] Query marker FASTA was written to OceanDNA-b31316/markers.fasta
[2023-03-15 15:06:37,783] [INFO] Task started: Blastn
[2023-03-15 15:06:37,783] [INFO] Running command: blastn -query OceanDNA-b31316/markers.fasta -db /var/lib/cwl/stg232f2b89-c2dd-4a59-94d3-9abcc6777134/dqc_reference/reference_markers.fasta -out OceanDNA-b31316/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:06:38,444] [INFO] Task succeeded: Blastn
[2023-03-15 15:06:38,452] [INFO] Selected 21 target genomes.
[2023-03-15 15:06:38,453] [INFO] Target genome list was writen to OceanDNA-b31316/target_genomes.txt
[2023-03-15 15:06:38,464] [INFO] Task started: fastANI
[2023-03-15 15:06:38,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg583bf0a3-9aae-4943-9987-c7f1802476ee/OceanDNA-b31316.fa --refList OceanDNA-b31316/target_genomes.txt --output OceanDNA-b31316/fastani_result.tsv --threads 1
[2023-03-15 15:06:48,636] [INFO] Task succeeded: fastANI
[2023-03-15 15:06:48,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg232f2b89-c2dd-4a59-94d3-9abcc6777134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:06:48,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg232f2b89-c2dd-4a59-94d3-9abcc6777134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:06:48,637] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:06:48,637] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:06:48,637] [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
--------------------------------------------------------------------------------
[2023-03-15 15:06:48,640] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31316/tc_result.tsv
[2023-03-15 15:06:48,644] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:06:48,645] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:06:48,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg232f2b89-c2dd-4a59-94d3-9abcc6777134/dqc_reference/checkm_data
[2023-03-15 15:06:48,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:06:48,713] [INFO] Task started: CheckM
[2023-03-15 15:06:48,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31316/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31316/checkm_input OceanDNA-b31316/checkm_result
[2023-03-15 15:07:05,207] [INFO] Task succeeded: CheckM
[2023-03-15 15:07:05,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 13.02%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-15 15:07:05,531] [INFO] ===== Completeness check finished =====
[2023-03-15 15:07:05,531] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:07:05,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31316/markers.fasta)
[2023-03-15 15:07:05,533] [INFO] Task started: Blastn
[2023-03-15 15:07:05,533] [INFO] Running command: blastn -query OceanDNA-b31316/markers.fasta -db /var/lib/cwl/stg232f2b89-c2dd-4a59-94d3-9abcc6777134/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31316/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:07:06,336] [INFO] Task succeeded: Blastn
[2023-03-15 15:07:06,343] [INFO] Selected 16 target genomes.
[2023-03-15 15:07:06,343] [INFO] Target genome list was writen to OceanDNA-b31316/target_genomes_gtdb.txt
[2023-03-15 15:07:06,365] [INFO] Task started: fastANI
[2023-03-15 15:07:06,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg583bf0a3-9aae-4943-9987-c7f1802476ee/OceanDNA-b31316.fa --refList OceanDNA-b31316/target_genomes_gtdb.txt --output OceanDNA-b31316/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:07:10,114] [INFO] Task succeeded: fastANI
[2023-03-15 15:07:10,117] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:07:10,117] [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_018659605.1	s__JADHOX01 sp018659605	99.4644	106	122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__JABIRX01;g__JADHOX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018659145.1	s__JADHOX01 sp018659145	78.5259	63	122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__JABIRX01;g__JADHOX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:07:10,120] [INFO] GTDB search result was written to OceanDNA-b31316/result_gtdb.tsv
[2023-03-15 15:07:10,124] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:07:10,129] [INFO] DFAST_QC result json was written to OceanDNA-b31316/dqc_result.json
[2023-03-15 15:07:10,129] [INFO] DFAST_QC completed!
[2023-03-15 15:07:10,129] [INFO] Total running time: 0h0m36s