[2023-03-14 12:25:41,520] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,521] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,521] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb065808-0e2b-42d7-b726-d9de58cfae5f/dqc_reference
[2023-03-14 12:25:42,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,640] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,640] [INFO] Running command: cat /var/lib/cwl/stg820ad1d0-ef9b-46ca-a5c1-5f197638445b/OceanDNA-b11611.fa | prodigal -d OceanDNA-b11611/cds.fna -a OceanDNA-b11611/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:26:05,417] [INFO] Task succeeded: Prodigal
[2023-03-14 12:26:05,417] [INFO] Task started: HMMsearch
[2023-03-14 12:26:05,417] [INFO] Running command: hmmsearch --tblout OceanDNA-b11611/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb065808-0e2b-42d7-b726-d9de58cfae5f/dqc_reference/reference_markers.hmm OceanDNA-b11611/protein.faa > /dev/null
[2023-03-14 12:26:05,627] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:26:05,628] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg820ad1d0-ef9b-46ca-a5c1-5f197638445b/OceanDNA-b11611.fa]
[2023-03-14 12:26:05,648] [INFO] Query marker FASTA was written to OceanDNA-b11611/markers.fasta
[2023-03-14 12:26:05,649] [INFO] Task started: Blastn
[2023-03-14 12:26:05,649] [INFO] Running command: blastn -query OceanDNA-b11611/markers.fasta -db /var/lib/cwl/stgeb065808-0e2b-42d7-b726-d9de58cfae5f/dqc_reference/reference_markers.fasta -out OceanDNA-b11611/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:06,177] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:06,178] [INFO] Selected 22 target genomes.
[2023-03-14 12:26:06,178] [INFO] Target genome list was writen to OceanDNA-b11611/target_genomes.txt
[2023-03-14 12:26:06,191] [INFO] Task started: fastANI
[2023-03-14 12:26:06,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg820ad1d0-ef9b-46ca-a5c1-5f197638445b/OceanDNA-b11611.fa --refList OceanDNA-b11611/target_genomes.txt --output OceanDNA-b11611/fastani_result.tsv --threads 1
[2023-03-14 12:26:20,566] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:20,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb065808-0e2b-42d7-b726-d9de58cfae5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:20,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb065808-0e2b-42d7-b726-d9de58cfae5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:20,567] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:20,567] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:26:20,567] [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
--------------------------------------------------------------------------------
[2023-03-14 12:26:20,567] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11611/tc_result.tsv
[2023-03-14 12:26:20,567] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:20,568] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:20,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb065808-0e2b-42d7-b726-d9de58cfae5f/dqc_reference/checkm_data
[2023-03-14 12:26:20,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:20,610] [INFO] Task started: CheckM
[2023-03-14 12:26:20,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11611/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11611/checkm_input OceanDNA-b11611/checkm_result
[2023-03-14 12:27:21,416] [INFO] Task succeeded: CheckM
[2023-03-14 12:27:21,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:27:21,419] [INFO] ===== Completeness check finished =====
[2023-03-14 12:27:21,419] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:27:21,419] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11611/markers.fasta)
[2023-03-14 12:27:21,420] [INFO] Task started: Blastn
[2023-03-14 12:27:21,420] [INFO] Running command: blastn -query OceanDNA-b11611/markers.fasta -db /var/lib/cwl/stgeb065808-0e2b-42d7-b726-d9de58cfae5f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11611/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:27:22,181] [INFO] Task succeeded: Blastn
[2023-03-14 12:27:22,182] [INFO] Selected 30 target genomes.
[2023-03-14 12:27:22,182] [INFO] Target genome list was writen to OceanDNA-b11611/target_genomes_gtdb.txt
[2023-03-14 12:27:22,201] [INFO] Task started: fastANI
[2023-03-14 12:27:22,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg820ad1d0-ef9b-46ca-a5c1-5f197638445b/OceanDNA-b11611.fa --refList OceanDNA-b11611/target_genomes_gtdb.txt --output OceanDNA-b11611/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:27:38,635] [INFO] Task succeeded: fastANI
[2023-03-14 12:27:38,635] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:27:38,635] [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
--------------------------------------------------------------------------------
[2023-03-14 12:27:38,636] [INFO] GTDB search result was written to OceanDNA-b11611/result_gtdb.tsv
[2023-03-14 12:27:38,636] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:27:38,636] [INFO] DFAST_QC result json was written to OceanDNA-b11611/dqc_result.json
[2023-03-14 12:27:38,636] [INFO] DFAST_QC completed!
[2023-03-14 12:27:38,636] [INFO] Total running time: 0h1m57s