[2023-03-15 03:38:34,774] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:38:34,775] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:38:34,775] [INFO] DQC Reference Directory: /var/lib/cwl/stg99e7ca7f-0da5-4170-8a21-da676c56234e/dqc_reference
[2023-03-15 03:38:35,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:38:35,908] [INFO] Task started: Prodigal
[2023-03-15 03:38:35,908] [INFO] Running command: cat /var/lib/cwl/stgd1444cdd-3809-4305-be74-a9201cca0f73/OceanDNA-b46265.fa | prodigal -d OceanDNA-b46265/cds.fna -a OceanDNA-b46265/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:39:06,829] [INFO] Task succeeded: Prodigal
[2023-03-15 03:39:06,830] [INFO] Task started: HMMsearch
[2023-03-15 03:39:06,830] [INFO] Running command: hmmsearch --tblout OceanDNA-b46265/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99e7ca7f-0da5-4170-8a21-da676c56234e/dqc_reference/reference_markers.hmm OceanDNA-b46265/protein.faa > /dev/null
[2023-03-15 03:39:07,030] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:39:07,031] [INFO] Found 6/6 markers.
[2023-03-15 03:39:07,062] [INFO] Query marker FASTA was written to OceanDNA-b46265/markers.fasta
[2023-03-15 03:39:07,064] [INFO] Task started: Blastn
[2023-03-15 03:39:07,064] [INFO] Running command: blastn -query OceanDNA-b46265/markers.fasta -db /var/lib/cwl/stg99e7ca7f-0da5-4170-8a21-da676c56234e/dqc_reference/reference_markers.fasta -out OceanDNA-b46265/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:39:08,395] [INFO] Task succeeded: Blastn
[2023-03-15 03:39:08,398] [INFO] Selected 18 target genomes.
[2023-03-15 03:39:08,399] [INFO] Target genome list was writen to OceanDNA-b46265/target_genomes.txt
[2023-03-15 03:39:08,472] [INFO] Task started: fastANI
[2023-03-15 03:39:08,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1444cdd-3809-4305-be74-a9201cca0f73/OceanDNA-b46265.fa --refList OceanDNA-b46265/target_genomes.txt --output OceanDNA-b46265/fastani_result.tsv --threads 1
[2023-03-15 03:39:20,429] [INFO] Task succeeded: fastANI
[2023-03-15 03:39:20,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99e7ca7f-0da5-4170-8a21-da676c56234e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:39:20,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99e7ca7f-0da5-4170-8a21-da676c56234e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:39:20,430] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:39:20,430] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:39:20,430] [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 03:39:20,431] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46265/tc_result.tsv
[2023-03-15 03:39:20,431] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:39:20,431] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:39:20,431] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99e7ca7f-0da5-4170-8a21-da676c56234e/dqc_reference/checkm_data
[2023-03-15 03:39:20,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:39:20,446] [INFO] Task started: CheckM
[2023-03-15 03:39:20,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46265/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46265/checkm_input OceanDNA-b46265/checkm_result
[2023-03-15 03:40:41,636] [INFO] Task succeeded: CheckM
[2023-03-15 03:40:41,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:40:41,670] [INFO] ===== Completeness check finished =====
[2023-03-15 03:40:41,670] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:40:41,670] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46265/markers.fasta)
[2023-03-15 03:40:41,671] [INFO] Task started: Blastn
[2023-03-15 03:40:41,671] [INFO] Running command: blastn -query OceanDNA-b46265/markers.fasta -db /var/lib/cwl/stg99e7ca7f-0da5-4170-8a21-da676c56234e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46265/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:40:42,625] [INFO] Task succeeded: Blastn
[2023-03-15 03:40:42,627] [INFO] Selected 24 target genomes.
[2023-03-15 03:40:42,627] [INFO] Target genome list was writen to OceanDNA-b46265/target_genomes_gtdb.txt
[2023-03-15 03:40:42,833] [INFO] Task started: fastANI
[2023-03-15 03:40:42,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1444cdd-3809-4305-be74-a9201cca0f73/OceanDNA-b46265.fa --refList OceanDNA-b46265/target_genomes_gtdb.txt --output OceanDNA-b46265/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:41:00,131] [INFO] Task succeeded: fastANI
[2023-03-15 03:41:00,133] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:41:00,134] [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_002686885.1	s__UBA7971 sp002686885	99.5408	1035	1082	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__AAA164-E04;g__UBA7971	95.0	98.29	95.01	0.90	0.82	6	conclusive
--------------------------------------------------------------------------------
[2023-03-15 03:41:00,134] [INFO] GTDB search result was written to OceanDNA-b46265/result_gtdb.tsv
[2023-03-15 03:41:00,135] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:41:00,136] [INFO] DFAST_QC result json was written to OceanDNA-b46265/dqc_result.json
[2023-03-15 03:41:00,136] [INFO] DFAST_QC completed!
[2023-03-15 03:41:00,136] [INFO] Total running time: 0h2m25s