[2023-03-15 23:42:29,662] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,663] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b0f6d78-0964-4dcd-91c0-b0e781139379/dqc_reference
[2023-03-15 23:42:31,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,277] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,278] [INFO] Running command: cat /var/lib/cwl/stgc0b288ec-a3d6-454b-93fb-d06ac01eb42d/OceanDNA-a4400.fa | prodigal -d OceanDNA-a4400/cds.fna -a OceanDNA-a4400/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:38,187] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:38,187] [INFO] Task started: HMMsearch
[2023-03-15 23:42:38,187] [INFO] Running command: hmmsearch --tblout OceanDNA-a4400/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b0f6d78-0964-4dcd-91c0-b0e781139379/dqc_reference/reference_markers.hmm OceanDNA-a4400/protein.faa > /dev/null
[2023-03-15 23:42:38,312] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:38,312] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc0b288ec-a3d6-454b-93fb-d06ac01eb42d/OceanDNA-a4400.fa]
[2023-03-15 23:42:38,321] [INFO] Query marker FASTA was written to OceanDNA-a4400/markers.fasta
[2023-03-15 23:42:38,323] [INFO] Task started: Blastn
[2023-03-15 23:42:38,323] [INFO] Running command: blastn -query OceanDNA-a4400/markers.fasta -db /var/lib/cwl/stg7b0f6d78-0964-4dcd-91c0-b0e781139379/dqc_reference/reference_markers.fasta -out OceanDNA-a4400/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:38,748] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:38,749] [INFO] Selected 0 target genomes.
[2023-03-15 23:42:38,749] [INFO] Target genome list was writen to OceanDNA-a4400/target_genomes.txt
[2023-03-15 23:42:38,749] [ERROR] File is empty. [OceanDNA-a4400/target_genomes.txt]
[2023-03-15 23:42:38,749] [ERROR] Task failed. No target genome found.
[2023-03-15 23:42:38,749] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:42:38,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b0f6d78-0964-4dcd-91c0-b0e781139379/dqc_reference/checkm_data
[2023-03-15 23:42:38,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:42:38,762] [INFO] Task started: CheckM
[2023-03-15 23:42:38,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4400/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4400/checkm_input OceanDNA-a4400/checkm_result
[2023-03-15 23:43:03,056] [INFO] Task succeeded: CheckM
[2023-03-15 23:43:03,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:43:03,058] [INFO] ===== Completeness check finished =====
[2023-03-15 23:43:03,058] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:43:03,059] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4400/markers.fasta)
[2023-03-15 23:43:03,060] [INFO] Task started: Blastn
[2023-03-15 23:43:03,060] [INFO] Running command: blastn -query OceanDNA-a4400/markers.fasta -db /var/lib/cwl/stg7b0f6d78-0964-4dcd-91c0-b0e781139379/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4400/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:43:03,513] [INFO] Task succeeded: Blastn
[2023-03-15 23:43:03,514] [INFO] Selected 1 target genomes.
[2023-03-15 23:43:03,514] [INFO] Target genome list was writen to OceanDNA-a4400/target_genomes_gtdb.txt
[2023-03-15 23:43:03,515] [INFO] Task started: fastANI
[2023-03-15 23:43:03,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0b288ec-a3d6-454b-93fb-d06ac01eb42d/OceanDNA-a4400.fa --refList OceanDNA-a4400/target_genomes_gtdb.txt --output OceanDNA-a4400/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:43:03,916] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:03,917] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:43:03,918] [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_002718695.1	s__MGIIb-O3 sp002718695	98.2801	351	391	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-15 23:43:03,918] [INFO] GTDB search result was written to OceanDNA-a4400/result_gtdb.tsv
[2023-03-15 23:43:03,918] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:43:03,918] [INFO] DFAST_QC result json was written to OceanDNA-a4400/dqc_result.json
[2023-03-15 23:43:03,918] [INFO] DFAST_QC completed!
[2023-03-15 23:43:03,918] [INFO] Total running time: 0h0m34s