[2023-03-15 08:59:47,106] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,106] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,106] [INFO] DQC Reference Directory: /var/lib/cwl/stgce1f5a4b-c09b-4070-89b2-59cf9687a04f/dqc_reference
[2023-03-15 08:59:48,187] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,187] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,187] [INFO] Running command: cat /var/lib/cwl/stgcafc65af-7bdf-42bd-86c9-c9266d072fac/OceanDNA-b3626.fa | prodigal -d OceanDNA-b3626/cds.fna -a OceanDNA-b3626/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:08,087] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:08,088] [INFO] Task started: HMMsearch
[2023-03-15 09:00:08,088] [INFO] Running command: hmmsearch --tblout OceanDNA-b3626/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce1f5a4b-c09b-4070-89b2-59cf9687a04f/dqc_reference/reference_markers.hmm OceanDNA-b3626/protein.faa > /dev/null
[2023-03-15 09:00:08,278] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:08,279] [INFO] Found 6/6 markers.
[2023-03-15 09:00:08,302] [INFO] Query marker FASTA was written to OceanDNA-b3626/markers.fasta
[2023-03-15 09:00:08,302] [INFO] Task started: Blastn
[2023-03-15 09:00:08,302] [INFO] Running command: blastn -query OceanDNA-b3626/markers.fasta -db /var/lib/cwl/stgce1f5a4b-c09b-4070-89b2-59cf9687a04f/dqc_reference/reference_markers.fasta -out OceanDNA-b3626/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:08,838] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:08,839] [INFO] Selected 23 target genomes.
[2023-03-15 09:00:08,839] [INFO] Target genome list was writen to OceanDNA-b3626/target_genomes.txt
[2023-03-15 09:00:08,857] [INFO] Task started: fastANI
[2023-03-15 09:00:08,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgcafc65af-7bdf-42bd-86c9-c9266d072fac/OceanDNA-b3626.fa --refList OceanDNA-b3626/target_genomes.txt --output OceanDNA-b3626/fastani_result.tsv --threads 1
[2023-03-15 09:00:25,692] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:25,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce1f5a4b-c09b-4070-89b2-59cf9687a04f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:25,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce1f5a4b-c09b-4070-89b2-59cf9687a04f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:25,693] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:25,693] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:00:25,693] [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 09:00:25,693] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3626/tc_result.tsv
[2023-03-15 09:00:25,693] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:25,693] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:25,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce1f5a4b-c09b-4070-89b2-59cf9687a04f/dqc_reference/checkm_data
[2023-03-15 09:00:25,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:25,701] [INFO] Task started: CheckM
[2023-03-15 09:00:25,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3626/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3626/checkm_input OceanDNA-b3626/checkm_result
[2023-03-15 09:01:16,862] [INFO] Task succeeded: CheckM
[2023-03-15 09:01:16,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.05%
Contamintation: 2.46%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 09:01:16,865] [INFO] ===== Completeness check finished =====
[2023-03-15 09:01:16,866] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:01:16,866] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3626/markers.fasta)
[2023-03-15 09:01:16,866] [INFO] Task started: Blastn
[2023-03-15 09:01:16,866] [INFO] Running command: blastn -query OceanDNA-b3626/markers.fasta -db /var/lib/cwl/stgce1f5a4b-c09b-4070-89b2-59cf9687a04f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3626/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:01:17,605] [INFO] Task succeeded: Blastn
[2023-03-15 09:01:17,606] [INFO] Selected 30 target genomes.
[2023-03-15 09:01:17,606] [INFO] Target genome list was writen to OceanDNA-b3626/target_genomes_gtdb.txt
[2023-03-15 09:01:17,719] [INFO] Task started: fastANI
[2023-03-15 09:01:17,719] [INFO] Running command: fastANI --query /var/lib/cwl/stgcafc65af-7bdf-42bd-86c9-c9266d072fac/OceanDNA-b3626.fa --refList OceanDNA-b3626/target_genomes_gtdb.txt --output OceanDNA-b3626/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:01:34,376] [INFO] Task succeeded: fastANI
[2023-03-15 09:01:34,377] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:01:34,377] [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
--------------------------------------------------------------------------------
[2023-03-15 09:01:34,377] [INFO] GTDB search result was written to OceanDNA-b3626/result_gtdb.tsv
[2023-03-15 09:01:34,377] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:01:34,377] [INFO] DFAST_QC result json was written to OceanDNA-b3626/dqc_result.json
[2023-03-15 09:01:34,377] [INFO] DFAST_QC completed!
[2023-03-15 09:01:34,377] [INFO] Total running time: 0h1m47s