[2023-03-19 02:40:15,840] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e2edea7-832c-4430-b619-88c90f9d8537/dqc_reference
[2023-03-19 02:40:17,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:17,564] [INFO] Task started: Prodigal
[2023-03-19 02:40:17,564] [INFO] Running command: cat /var/lib/cwl/stga6d59041-0063-4373-a9c5-f0e44e2aac79/OceanDNA-b19701.fa | prodigal -d OceanDNA-b19701/cds.fna -a OceanDNA-b19701/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:22,974] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:22,974] [INFO] Task started: HMMsearch
[2023-03-19 02:40:22,974] [INFO] Running command: hmmsearch --tblout OceanDNA-b19701/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e2edea7-832c-4430-b619-88c90f9d8537/dqc_reference/reference_markers.hmm OceanDNA-b19701/protein.faa > /dev/null
[2023-03-19 02:40:23,089] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:23,090] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga6d59041-0063-4373-a9c5-f0e44e2aac79/OceanDNA-b19701.fa]
[2023-03-19 02:40:23,103] [INFO] Query marker FASTA was written to OceanDNA-b19701/markers.fasta
[2023-03-19 02:40:23,104] [INFO] Task started: Blastn
[2023-03-19 02:40:23,104] [INFO] Running command: blastn -query OceanDNA-b19701/markers.fasta -db /var/lib/cwl/stg4e2edea7-832c-4430-b619-88c90f9d8537/dqc_reference/reference_markers.fasta -out OceanDNA-b19701/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:23,702] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:23,703] [INFO] Selected 0 target genomes.
[2023-03-19 02:40:23,703] [INFO] Target genome list was writen to OceanDNA-b19701/target_genomes.txt
[2023-03-19 02:40:23,703] [ERROR] File is empty. [OceanDNA-b19701/target_genomes.txt]
[2023-03-19 02:40:23,703] [ERROR] Task failed. No target genome found.
[2023-03-19 02:40:23,703] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:40:23,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e2edea7-832c-4430-b619-88c90f9d8537/dqc_reference/checkm_data
[2023-03-19 02:40:23,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:40:23,718] [INFO] Task started: CheckM
[2023-03-19 02:40:23,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19701/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19701/checkm_input OceanDNA-b19701/checkm_result
[2023-03-19 02:40:45,619] [INFO] Task succeeded: CheckM
[2023-03-19 02:40:45,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.03%
Contamintation: 5.45%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:40:45,634] [INFO] ===== Completeness check finished =====
[2023-03-19 02:40:45,634] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:40:45,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19701/markers.fasta)
[2023-03-19 02:40:45,636] [INFO] Task started: Blastn
[2023-03-19 02:40:45,636] [INFO] Running command: blastn -query OceanDNA-b19701/markers.fasta -db /var/lib/cwl/stg4e2edea7-832c-4430-b619-88c90f9d8537/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19701/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:46,234] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:46,237] [INFO] Selected 1 target genomes.
[2023-03-19 02:40:46,237] [INFO] Target genome list was writen to OceanDNA-b19701/target_genomes_gtdb.txt
[2023-03-19 02:40:46,240] [INFO] Task started: fastANI
[2023-03-19 02:40:46,240] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d59041-0063-4373-a9c5-f0e44e2aac79/OceanDNA-b19701.fa --refList OceanDNA-b19701/target_genomes_gtdb.txt --output OceanDNA-b19701/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:40:46,523] [INFO] Task succeeded: fastANI
[2023-03-19 02:40:46,525] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:40:46,525] [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_002717915.1	s__GCA-002717915 sp002717915	92.5045	168	296	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002717915	95.0	98.06	98.06	0.68	0.68	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:40:46,526] [INFO] GTDB search result was written to OceanDNA-b19701/result_gtdb.tsv
[2023-03-19 02:40:46,528] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:40:46,529] [INFO] DFAST_QC result json was written to OceanDNA-b19701/dqc_result.json
[2023-03-19 02:40:46,529] [INFO] DFAST_QC completed!
[2023-03-19 02:40:46,529] [INFO] Total running time: 0h0m31s