[2023-03-15 13:00:04,939] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:00:04,939] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:00:04,940] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6bb8b8f-4a8c-476e-a7e0-c285cfe214bf/dqc_reference
[2023-03-15 13:00:06,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:00:06,091] [INFO] Task started: Prodigal
[2023-03-15 13:00:06,091] [INFO] Running command: cat /var/lib/cwl/stg9cc7cd72-f858-4715-8abf-65b223e5e34b/OceanDNA-b24075.fa | prodigal -d OceanDNA-b24075/cds.fna -a OceanDNA-b24075/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:00:26,943] [INFO] Task succeeded: Prodigal
[2023-03-15 13:00:26,944] [INFO] Task started: HMMsearch
[2023-03-15 13:00:26,944] [INFO] Running command: hmmsearch --tblout OceanDNA-b24075/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6bb8b8f-4a8c-476e-a7e0-c285cfe214bf/dqc_reference/reference_markers.hmm OceanDNA-b24075/protein.faa > /dev/null
[2023-03-15 13:00:27,148] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:00:27,149] [INFO] Found 6/6 markers.
[2023-03-15 13:00:27,168] [INFO] Query marker FASTA was written to OceanDNA-b24075/markers.fasta
[2023-03-15 13:00:27,168] [INFO] Task started: Blastn
[2023-03-15 13:00:27,168] [INFO] Running command: blastn -query OceanDNA-b24075/markers.fasta -db /var/lib/cwl/stgf6bb8b8f-4a8c-476e-a7e0-c285cfe214bf/dqc_reference/reference_markers.fasta -out OceanDNA-b24075/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:00:27,773] [INFO] Task succeeded: Blastn
[2023-03-15 13:00:27,774] [INFO] Selected 29 target genomes.
[2023-03-15 13:00:27,774] [INFO] Target genome list was writen to OceanDNA-b24075/target_genomes.txt
[2023-03-15 13:00:27,790] [INFO] Task started: fastANI
[2023-03-15 13:00:27,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc7cd72-f858-4715-8abf-65b223e5e34b/OceanDNA-b24075.fa --refList OceanDNA-b24075/target_genomes.txt --output OceanDNA-b24075/fastani_result.tsv --threads 1
[2023-03-15 13:00:46,067] [INFO] Task succeeded: fastANI
[2023-03-15 13:00:46,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6bb8b8f-4a8c-476e-a7e0-c285cfe214bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:00:46,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6bb8b8f-4a8c-476e-a7e0-c285cfe214bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:00:46,068] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:00:46,068] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:00:46,068] [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 13:00:46,068] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24075/tc_result.tsv
[2023-03-15 13:00:46,068] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:00:46,068] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:00:46,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6bb8b8f-4a8c-476e-a7e0-c285cfe214bf/dqc_reference/checkm_data
[2023-03-15 13:00:46,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:00:46,076] [INFO] Task started: CheckM
[2023-03-15 13:00:46,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24075/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24075/checkm_input OceanDNA-b24075/checkm_result
[2023-03-15 13:01:38,509] [INFO] Task succeeded: CheckM
[2023-03-15 13:01:38,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:01:38,539] [INFO] ===== Completeness check finished =====
[2023-03-15 13:01:38,539] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:01:38,539] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24075/markers.fasta)
[2023-03-15 13:01:38,541] [INFO] Task started: Blastn
[2023-03-15 13:01:38,541] [INFO] Running command: blastn -query OceanDNA-b24075/markers.fasta -db /var/lib/cwl/stgf6bb8b8f-4a8c-476e-a7e0-c285cfe214bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24075/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:01:39,929] [INFO] Task succeeded: Blastn
[2023-03-15 13:01:39,931] [INFO] Selected 24 target genomes.
[2023-03-15 13:01:39,932] [INFO] Target genome list was writen to OceanDNA-b24075/target_genomes_gtdb.txt
[2023-03-15 13:01:40,047] [INFO] Task started: fastANI
[2023-03-15 13:01:40,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc7cd72-f858-4715-8abf-65b223e5e34b/OceanDNA-b24075.fa --refList OceanDNA-b24075/target_genomes_gtdb.txt --output OceanDNA-b24075/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:01:52,778] [INFO] Task succeeded: fastANI
[2023-03-15 13:01:52,781] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:01:52,781] [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_002720855.1	s__GCA-2720855 sp002720855	99.9736	1125	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__GCA-2720855	95.0	99.96	99.96	0.99	0.99	2	conclusive
GCA_012103315.1	s__WLWZ01 sp012103315	77.2169	264	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WLWZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660305.1	s__JABJKO01 sp018660305	76.0732	64	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:01:52,782] [INFO] GTDB search result was written to OceanDNA-b24075/result_gtdb.tsv
[2023-03-15 13:01:52,784] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:01:52,787] [INFO] DFAST_QC result json was written to OceanDNA-b24075/dqc_result.json
[2023-03-15 13:01:52,787] [INFO] DFAST_QC completed!
[2023-03-15 13:01:52,787] [INFO] Total running time: 0h1m48s