[2023-03-18 00:58:44,624] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:58:44,624] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:58:44,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a3824f1-3294-4f41-ab0f-3313b6f54ea3/dqc_reference
[2023-03-18 00:58:46,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:58:46,296] [INFO] Task started: Prodigal
[2023-03-18 00:58:46,296] [INFO] Running command: cat /var/lib/cwl/stg2d6ff8d5-953b-4403-9493-e70cda0bc041/OceanDNA-b20991.fa | prodigal -d OceanDNA-b20991/cds.fna -a OceanDNA-b20991/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:58:59,562] [INFO] Task succeeded: Prodigal
[2023-03-18 00:58:59,562] [INFO] Task started: HMMsearch
[2023-03-18 00:58:59,562] [INFO] Running command: hmmsearch --tblout OceanDNA-b20991/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a3824f1-3294-4f41-ab0f-3313b6f54ea3/dqc_reference/reference_markers.hmm OceanDNA-b20991/protein.faa > /dev/null
[2023-03-18 00:58:59,751] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:58:59,752] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2d6ff8d5-953b-4403-9493-e70cda0bc041/OceanDNA-b20991.fa]
[2023-03-18 00:58:59,776] [INFO] Query marker FASTA was written to OceanDNA-b20991/markers.fasta
[2023-03-18 00:58:59,777] [INFO] Task started: Blastn
[2023-03-18 00:58:59,777] [INFO] Running command: blastn -query OceanDNA-b20991/markers.fasta -db /var/lib/cwl/stg1a3824f1-3294-4f41-ab0f-3313b6f54ea3/dqc_reference/reference_markers.fasta -out OceanDNA-b20991/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:00,299] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:00,301] [INFO] Selected 18 target genomes.
[2023-03-18 00:59:00,301] [INFO] Target genome list was writen to OceanDNA-b20991/target_genomes.txt
[2023-03-18 00:59:00,310] [INFO] Task started: fastANI
[2023-03-18 00:59:00,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d6ff8d5-953b-4403-9493-e70cda0bc041/OceanDNA-b20991.fa --refList OceanDNA-b20991/target_genomes.txt --output OceanDNA-b20991/fastani_result.tsv --threads 1
[2023-03-18 00:59:13,317] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:13,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a3824f1-3294-4f41-ab0f-3313b6f54ea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:59:13,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a3824f1-3294-4f41-ab0f-3313b6f54ea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:59:13,318] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:59:13,318] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:59:13,318] [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
--------------------------------------------------------------------------------
[2023-03-18 00:59:13,319] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20991/tc_result.tsv
[2023-03-18 00:59:13,319] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:59:13,319] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:59:13,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a3824f1-3294-4f41-ab0f-3313b6f54ea3/dqc_reference/checkm_data
[2023-03-18 00:59:13,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:59:13,445] [INFO] Task started: CheckM
[2023-03-18 00:59:13,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20991/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20991/checkm_input OceanDNA-b20991/checkm_result
[2023-03-18 00:59:50,516] [INFO] Task succeeded: CheckM
[2023-03-18 00:59:50,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:59:50,522] [INFO] ===== Completeness check finished =====
[2023-03-18 00:59:50,522] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:59:50,522] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20991/markers.fasta)
[2023-03-18 00:59:50,523] [INFO] Task started: Blastn
[2023-03-18 00:59:50,523] [INFO] Running command: blastn -query OceanDNA-b20991/markers.fasta -db /var/lib/cwl/stg1a3824f1-3294-4f41-ab0f-3313b6f54ea3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20991/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:51,257] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:51,259] [INFO] Selected 21 target genomes.
[2023-03-18 00:59:51,259] [INFO] Target genome list was writen to OceanDNA-b20991/target_genomes_gtdb.txt
[2023-03-18 00:59:51,331] [INFO] Task started: fastANI
[2023-03-18 00:59:51,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d6ff8d5-953b-4403-9493-e70cda0bc041/OceanDNA-b20991.fa --refList OceanDNA-b20991/target_genomes_gtdb.txt --output OceanDNA-b20991/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:00:04,501] [INFO] Task succeeded: fastANI
[2023-03-18 01:00:04,501] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:00:04,501] [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
--------------------------------------------------------------------------------
[2023-03-18 01:00:04,502] [INFO] GTDB search result was written to OceanDNA-b20991/result_gtdb.tsv
[2023-03-18 01:00:04,502] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:00:04,502] [INFO] DFAST_QC result json was written to OceanDNA-b20991/dqc_result.json
[2023-03-18 01:00:04,503] [INFO] DFAST_QC completed!
[2023-03-18 01:00:04,503] [INFO] Total running time: 0h1m20s