[2023-03-15 08:19:26,368] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:19:26,368] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:19:26,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ae282db-18ab-4737-8840-975f33a6569f/dqc_reference
[2023-03-15 08:19:27,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:19:27,461] [INFO] Task started: Prodigal
[2023-03-15 08:19:27,461] [INFO] Running command: cat /var/lib/cwl/stg473a353a-32e5-44bb-bd9a-3d15ec26a343/OceanDNA-b22859.fa | prodigal -d OceanDNA-b22859/cds.fna -a OceanDNA-b22859/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:19:45,718] [INFO] Task succeeded: Prodigal
[2023-03-15 08:19:45,718] [INFO] Task started: HMMsearch
[2023-03-15 08:19:45,718] [INFO] Running command: hmmsearch --tblout OceanDNA-b22859/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ae282db-18ab-4737-8840-975f33a6569f/dqc_reference/reference_markers.hmm OceanDNA-b22859/protein.faa > /dev/null
[2023-03-15 08:19:45,937] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:19:45,938] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg473a353a-32e5-44bb-bd9a-3d15ec26a343/OceanDNA-b22859.fa]
[2023-03-15 08:19:45,972] [INFO] Query marker FASTA was written to OceanDNA-b22859/markers.fasta
[2023-03-15 08:19:45,974] [INFO] Task started: Blastn
[2023-03-15 08:19:45,974] [INFO] Running command: blastn -query OceanDNA-b22859/markers.fasta -db /var/lib/cwl/stg4ae282db-18ab-4737-8840-975f33a6569f/dqc_reference/reference_markers.fasta -out OceanDNA-b22859/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:19:46,489] [INFO] Task succeeded: Blastn
[2023-03-15 08:19:46,489] [INFO] Selected 0 target genomes.
[2023-03-15 08:19:46,489] [INFO] Target genome list was writen to OceanDNA-b22859/target_genomes.txt
[2023-03-15 08:19:46,489] [ERROR] File is empty. [OceanDNA-b22859/target_genomes.txt]
[2023-03-15 08:19:46,489] [ERROR] Task failed. No target genome found.
[2023-03-15 08:19:46,490] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:19:46,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ae282db-18ab-4737-8840-975f33a6569f/dqc_reference/checkm_data
[2023-03-15 08:19:46,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:19:46,506] [INFO] Task started: CheckM
[2023-03-15 08:19:46,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22859/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22859/checkm_input OceanDNA-b22859/checkm_result
[2023-03-15 08:20:35,661] [INFO] Task succeeded: CheckM
[2023-03-15 08:20:35,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:20:35,664] [INFO] ===== Completeness check finished =====
[2023-03-15 08:20:35,665] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:20:35,665] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22859/markers.fasta)
[2023-03-15 08:20:35,666] [INFO] Task started: Blastn
[2023-03-15 08:20:35,666] [INFO] Running command: blastn -query OceanDNA-b22859/markers.fasta -db /var/lib/cwl/stg4ae282db-18ab-4737-8840-975f33a6569f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22859/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:20:36,441] [INFO] Task succeeded: Blastn
[2023-03-15 08:20:36,442] [INFO] Selected 10 target genomes.
[2023-03-15 08:20:36,442] [INFO] Target genome list was writen to OceanDNA-b22859/target_genomes_gtdb.txt
[2023-03-15 08:20:36,449] [INFO] Task started: fastANI
[2023-03-15 08:20:36,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg473a353a-32e5-44bb-bd9a-3d15ec26a343/OceanDNA-b22859.fa --refList OceanDNA-b22859/target_genomes_gtdb.txt --output OceanDNA-b22859/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:20:44,139] [INFO] Task succeeded: fastANI
[2023-03-15 08:20:44,141] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:20:44,141] [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_003670925.1	s__SXXK01 sp003670925	76.884	118	545	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:20:44,141] [INFO] GTDB search result was written to OceanDNA-b22859/result_gtdb.tsv
[2023-03-15 08:20:44,142] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:20:44,142] [INFO] DFAST_QC result json was written to OceanDNA-b22859/dqc_result.json
[2023-03-15 08:20:44,142] [INFO] DFAST_QC completed!
[2023-03-15 08:20:44,142] [INFO] Total running time: 0h1m18s