[2023-03-14 10:55:58,906] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,906] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg56068353-3826-4730-b551-d618b10fb47e/dqc_reference
[2023-03-14 10:56:00,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,680] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,680] [INFO] Running command: cat /var/lib/cwl/stg1c5d7cde-a5f7-47bb-8bad-c163ce4bba33/OceanDNA-b14653.fa | prodigal -d OceanDNA-b14653/cds.fna -a OceanDNA-b14653/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:08,051] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:08,052] [INFO] Task started: HMMsearch
[2023-03-14 10:56:08,052] [INFO] Running command: hmmsearch --tblout OceanDNA-b14653/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56068353-3826-4730-b551-d618b10fb47e/dqc_reference/reference_markers.hmm OceanDNA-b14653/protein.faa > /dev/null
[2023-03-14 10:56:08,196] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:08,196] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1c5d7cde-a5f7-47bb-8bad-c163ce4bba33/OceanDNA-b14653.fa]
[2023-03-14 10:56:08,208] [INFO] Query marker FASTA was written to OceanDNA-b14653/markers.fasta
[2023-03-14 10:56:08,208] [INFO] Task started: Blastn
[2023-03-14 10:56:08,208] [INFO] Running command: blastn -query OceanDNA-b14653/markers.fasta -db /var/lib/cwl/stg56068353-3826-4730-b551-d618b10fb47e/dqc_reference/reference_markers.fasta -out OceanDNA-b14653/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:08,640] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:08,640] [INFO] Selected 0 target genomes.
[2023-03-14 10:56:08,641] [INFO] Target genome list was writen to OceanDNA-b14653/target_genomes.txt
[2023-03-14 10:56:08,641] [ERROR] File is empty. [OceanDNA-b14653/target_genomes.txt]
[2023-03-14 10:56:08,641] [ERROR] Task failed. No target genome found.
[2023-03-14 10:56:08,641] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:08,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56068353-3826-4730-b551-d618b10fb47e/dqc_reference/checkm_data
[2023-03-14 10:56:08,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:08,647] [INFO] Task started: CheckM
[2023-03-14 10:56:08,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14653/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14653/checkm_input OceanDNA-b14653/checkm_result
[2023-03-14 10:56:32,525] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:32,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:32,527] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:32,527] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:32,527] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14653/markers.fasta)
[2023-03-14 10:56:32,527] [INFO] Task started: Blastn
[2023-03-14 10:56:32,527] [INFO] Running command: blastn -query OceanDNA-b14653/markers.fasta -db /var/lib/cwl/stg56068353-3826-4730-b551-d618b10fb47e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14653/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:32,992] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:32,993] [INFO] Selected 9 target genomes.
[2023-03-14 10:56:32,993] [INFO] Target genome list was writen to OceanDNA-b14653/target_genomes_gtdb.txt
[2023-03-14 10:56:33,005] [INFO] Task started: fastANI
[2023-03-14 10:56:33,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5d7cde-a5f7-47bb-8bad-c163ce4bba33/OceanDNA-b14653.fa --refList OceanDNA-b14653/target_genomes_gtdb.txt --output OceanDNA-b14653/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:36,487] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:36,490] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:56:36,490] [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_002313245.1	s__UBA9455 sp002313245	84.1325	300	427	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA9455	95.0	97.93	97.22	0.78	0.67	5	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:36,490] [INFO] GTDB search result was written to OceanDNA-b14653/result_gtdb.tsv
[2023-03-14 10:56:36,490] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:36,490] [INFO] DFAST_QC result json was written to OceanDNA-b14653/dqc_result.json
[2023-03-14 10:56:36,491] [INFO] DFAST_QC completed!
[2023-03-14 10:56:36,491] [INFO] Total running time: 0h0m38s