[2023-03-17 11:08:00,267] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,268] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg96f63d79-d664-4017-a207-1fd3a72d833c/dqc_reference
[2023-03-17 11:08:01,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,421] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,421] [INFO] Running command: cat /var/lib/cwl/stg8126e76f-b165-42a9-9cb6-c4551ead00ef/OceanDNA-b32517.fa | prodigal -d OceanDNA-b32517/cds.fna -a OceanDNA-b32517/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:06,337] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:06,337] [INFO] Task started: HMMsearch
[2023-03-17 11:08:06,337] [INFO] Running command: hmmsearch --tblout OceanDNA-b32517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96f63d79-d664-4017-a207-1fd3a72d833c/dqc_reference/reference_markers.hmm OceanDNA-b32517/protein.faa > /dev/null
[2023-03-17 11:08:06,523] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:06,524] [INFO] Found 6/6 markers.
[2023-03-17 11:08:06,543] [INFO] Query marker FASTA was written to OceanDNA-b32517/markers.fasta
[2023-03-17 11:08:06,545] [INFO] Task started: Blastn
[2023-03-17 11:08:06,545] [INFO] Running command: blastn -query OceanDNA-b32517/markers.fasta -db /var/lib/cwl/stg96f63d79-d664-4017-a207-1fd3a72d833c/dqc_reference/reference_markers.fasta -out OceanDNA-b32517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:07,117] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:07,121] [INFO] Selected 14 target genomes.
[2023-03-17 11:08:07,122] [INFO] Target genome list was writen to OceanDNA-b32517/target_genomes.txt
[2023-03-17 11:08:07,129] [INFO] Task started: fastANI
[2023-03-17 11:08:07,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg8126e76f-b165-42a9-9cb6-c4551ead00ef/OceanDNA-b32517.fa --refList OceanDNA-b32517/target_genomes.txt --output OceanDNA-b32517/fastani_result.tsv --threads 1
[2023-03-17 11:08:13,066] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:13,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96f63d79-d664-4017-a207-1fd3a72d833c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:13,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96f63d79-d664-4017-a207-1fd3a72d833c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:13,067] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:13,067] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:08:13,067] [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
--------------------------------------------------------------------------------
[2023-03-17 11:08:13,068] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32517/tc_result.tsv
[2023-03-17 11:08:13,071] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:13,071] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:13,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96f63d79-d664-4017-a207-1fd3a72d833c/dqc_reference/checkm_data
[2023-03-17 11:08:13,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:13,083] [INFO] Task started: CheckM
[2023-03-17 11:08:13,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32517/checkm_input OceanDNA-b32517/checkm_result
[2023-03-17 11:08:32,375] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:32,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:32,487] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:32,487] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:32,488] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32517/markers.fasta)
[2023-03-17 11:08:32,489] [INFO] Task started: Blastn
[2023-03-17 11:08:32,489] [INFO] Running command: blastn -query OceanDNA-b32517/markers.fasta -db /var/lib/cwl/stg96f63d79-d664-4017-a207-1fd3a72d833c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:33,591] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:33,593] [INFO] Selected 23 target genomes.
[2023-03-17 11:08:33,593] [INFO] Target genome list was writen to OceanDNA-b32517/target_genomes_gtdb.txt
[2023-03-17 11:08:34,014] [INFO] Task started: fastANI
[2023-03-17 11:08:34,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg8126e76f-b165-42a9-9cb6-c4551ead00ef/OceanDNA-b32517.fa --refList OceanDNA-b32517/target_genomes_gtdb.txt --output OceanDNA-b32517/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:08:39,915] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:39,917] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:08:39,918] [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_002711625.1	s__GCA-2711625 sp002711625	98.9202	254	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2711625	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902550225.1	s__GCA-2691245 sp902550225	76.1723	53	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:08:39,919] [INFO] GTDB search result was written to OceanDNA-b32517/result_gtdb.tsv
[2023-03-17 11:08:39,921] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:08:39,924] [INFO] DFAST_QC result json was written to OceanDNA-b32517/dqc_result.json
[2023-03-17 11:08:39,924] [INFO] DFAST_QC completed!
[2023-03-17 11:08:39,924] [INFO] Total running time: 0h0m40s