[2023-03-18 02:27:54,710] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:54,710] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:54,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg17f01314-71ed-4c6f-82a2-1ecd7c082c62/dqc_reference
[2023-03-18 02:27:55,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:55,952] [INFO] Task started: Prodigal
[2023-03-18 02:27:55,952] [INFO] Running command: cat /var/lib/cwl/stg93afc9da-3091-48f0-a0e8-4c6cdce3681d/OceanDNA-a8.fa | prodigal -d OceanDNA-a8/cds.fna -a OceanDNA-a8/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:03,262] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:03,262] [INFO] Task started: HMMsearch
[2023-03-18 02:28:03,262] [INFO] Running command: hmmsearch --tblout OceanDNA-a8/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17f01314-71ed-4c6f-82a2-1ecd7c082c62/dqc_reference/reference_markers.hmm OceanDNA-a8/protein.faa > /dev/null
[2023-03-18 02:28:03,392] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:03,393] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg93afc9da-3091-48f0-a0e8-4c6cdce3681d/OceanDNA-a8.fa]
[2023-03-18 02:28:03,402] [INFO] Query marker FASTA was written to OceanDNA-a8/markers.fasta
[2023-03-18 02:28:03,402] [INFO] Task started: Blastn
[2023-03-18 02:28:03,402] [INFO] Running command: blastn -query OceanDNA-a8/markers.fasta -db /var/lib/cwl/stg17f01314-71ed-4c6f-82a2-1ecd7c082c62/dqc_reference/reference_markers.fasta -out OceanDNA-a8/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:03,855] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:03,856] [INFO] Selected 0 target genomes.
[2023-03-18 02:28:03,856] [INFO] Target genome list was writen to OceanDNA-a8/target_genomes.txt
[2023-03-18 02:28:03,856] [ERROR] File is empty. [OceanDNA-a8/target_genomes.txt]
[2023-03-18 02:28:03,856] [ERROR] Task failed. No target genome found.
[2023-03-18 02:28:03,856] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:03,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17f01314-71ed-4c6f-82a2-1ecd7c082c62/dqc_reference/checkm_data
[2023-03-18 02:28:03,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:03,861] [INFO] Task started: CheckM
[2023-03-18 02:28:03,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a8/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a8/checkm_input OceanDNA-a8/checkm_result
[2023-03-18 02:28:27,545] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:27,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:27,548] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:27,548] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:27,548] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a8/markers.fasta)
[2023-03-18 02:28:27,548] [INFO] Task started: Blastn
[2023-03-18 02:28:27,548] [INFO] Running command: blastn -query OceanDNA-a8/markers.fasta -db /var/lib/cwl/stg17f01314-71ed-4c6f-82a2-1ecd7c082c62/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a8/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:27,948] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:27,949] [INFO] Selected 1 target genomes.
[2023-03-18 02:28:27,949] [INFO] Target genome list was writen to OceanDNA-a8/target_genomes_gtdb.txt
[2023-03-18 02:28:27,951] [INFO] Task started: fastANI
[2023-03-18 02:28:27,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg93afc9da-3091-48f0-a0e8-4c6cdce3681d/OceanDNA-a8.fa --refList OceanDNA-a8/target_genomes_gtdb.txt --output OceanDNA-a8/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:28,372] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:28,374] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:28:28,375] [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_002726865.1	s__GCA-2726865 sp002726865	97.6673	265	281	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__GCA-2726865	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 02:28:28,375] [INFO] GTDB search result was written to OceanDNA-a8/result_gtdb.tsv
[2023-03-18 02:28:28,375] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:28,375] [INFO] DFAST_QC result json was written to OceanDNA-a8/dqc_result.json
[2023-03-18 02:28:28,376] [INFO] DFAST_QC completed!
[2023-03-18 02:28:28,376] [INFO] Total running time: 0h0m34s