[2023-03-15 17:05:43,619] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:05:43,620] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:05:43,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg9875fc48-b16a-4946-b112-8cdcc555395e/dqc_reference
[2023-03-15 17:05:45,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:05:45,976] [INFO] Task started: Prodigal
[2023-03-15 17:05:45,976] [INFO] Running command: cat /var/lib/cwl/stg2edfa4bb-bf92-4a10-aab9-44726f9b282f/OceanDNA-b13108.fa | prodigal -d OceanDNA-b13108/cds.fna -a OceanDNA-b13108/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:06:06,969] [INFO] Task succeeded: Prodigal
[2023-03-15 17:06:06,970] [INFO] Task started: HMMsearch
[2023-03-15 17:06:06,970] [INFO] Running command: hmmsearch --tblout OceanDNA-b13108/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9875fc48-b16a-4946-b112-8cdcc555395e/dqc_reference/reference_markers.hmm OceanDNA-b13108/protein.faa > /dev/null
[2023-03-15 17:06:07,158] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:06:07,159] [INFO] Found 6/6 markers.
[2023-03-15 17:06:07,179] [INFO] Query marker FASTA was written to OceanDNA-b13108/markers.fasta
[2023-03-15 17:06:07,180] [INFO] Task started: Blastn
[2023-03-15 17:06:07,180] [INFO] Running command: blastn -query OceanDNA-b13108/markers.fasta -db /var/lib/cwl/stg9875fc48-b16a-4946-b112-8cdcc555395e/dqc_reference/reference_markers.fasta -out OceanDNA-b13108/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:06:07,720] [INFO] Task succeeded: Blastn
[2023-03-15 17:06:07,722] [INFO] Selected 20 target genomes.
[2023-03-15 17:06:07,722] [INFO] Target genome list was writen to OceanDNA-b13108/target_genomes.txt
[2023-03-15 17:06:07,747] [INFO] Task started: fastANI
[2023-03-15 17:06:07,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg2edfa4bb-bf92-4a10-aab9-44726f9b282f/OceanDNA-b13108.fa --refList OceanDNA-b13108/target_genomes.txt --output OceanDNA-b13108/fastani_result.tsv --threads 1
[2023-03-15 17:06:21,138] [INFO] Task succeeded: fastANI
[2023-03-15 17:06:21,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9875fc48-b16a-4946-b112-8cdcc555395e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:06:21,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9875fc48-b16a-4946-b112-8cdcc555395e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:06:21,139] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:06:21,139] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:06:21,139] [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 17:06:21,139] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13108/tc_result.tsv
[2023-03-15 17:06:21,140] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:06:21,140] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:06:21,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9875fc48-b16a-4946-b112-8cdcc555395e/dqc_reference/checkm_data
[2023-03-15 17:06:21,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:06:21,148] [INFO] Task started: CheckM
[2023-03-15 17:06:21,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13108/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13108/checkm_input OceanDNA-b13108/checkm_result
[2023-03-15 17:07:15,876] [INFO] Task succeeded: CheckM
[2023-03-15 17:07:15,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:07:15,900] [INFO] ===== Completeness check finished =====
[2023-03-15 17:07:15,900] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:07:15,901] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13108/markers.fasta)
[2023-03-15 17:07:15,902] [INFO] Task started: Blastn
[2023-03-15 17:07:15,902] [INFO] Running command: blastn -query OceanDNA-b13108/markers.fasta -db /var/lib/cwl/stg9875fc48-b16a-4946-b112-8cdcc555395e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13108/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:07:16,656] [INFO] Task succeeded: Blastn
[2023-03-15 17:07:16,660] [INFO] Selected 29 target genomes.
[2023-03-15 17:07:16,660] [INFO] Target genome list was writen to OceanDNA-b13108/target_genomes_gtdb.txt
[2023-03-15 17:07:16,729] [INFO] Task started: fastANI
[2023-03-15 17:07:16,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg2edfa4bb-bf92-4a10-aab9-44726f9b282f/OceanDNA-b13108.fa --refList OceanDNA-b13108/target_genomes_gtdb.txt --output OceanDNA-b13108/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:07:33,610] [INFO] Task succeeded: fastANI
[2023-03-15 17:07:33,612] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:07:33,612] [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_013204185.1	s__UBA10348 sp013204185	77.8919	132	861	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__UBA10348;g__UBA10348	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:07:33,614] [INFO] GTDB search result was written to OceanDNA-b13108/result_gtdb.tsv
[2023-03-15 17:07:33,615] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:07:33,616] [INFO] DFAST_QC result json was written to OceanDNA-b13108/dqc_result.json
[2023-03-15 17:07:33,617] [INFO] DFAST_QC completed!
[2023-03-15 17:07:33,617] [INFO] Total running time: 0h1m50s