[2023-03-16 04:54:07,049] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,049] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,049] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9cf194e-abe6-43fc-902f-74b4c9eaa0b8/dqc_reference
[2023-03-16 04:54:08,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,311] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,311] [INFO] Running command: cat /var/lib/cwl/stgbc0c86ec-631f-4dd7-8be9-2c8291e28764/OceanDNA-a4364.fa | prodigal -d OceanDNA-a4364/cds.fna -a OceanDNA-a4364/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:12,662] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:12,662] [INFO] Task started: HMMsearch
[2023-03-16 04:54:12,662] [INFO] Running command: hmmsearch --tblout OceanDNA-a4364/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9cf194e-abe6-43fc-902f-74b4c9eaa0b8/dqc_reference/reference_markers.hmm OceanDNA-a4364/protein.faa > /dev/null
[2023-03-16 04:54:12,831] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:12,831] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgbc0c86ec-631f-4dd7-8be9-2c8291e28764/OceanDNA-a4364.fa]
[2023-03-16 04:54:12,841] [INFO] Query marker FASTA was written to OceanDNA-a4364/markers.fasta
[2023-03-16 04:54:12,842] [INFO] Task started: Blastn
[2023-03-16 04:54:12,842] [INFO] Running command: blastn -query OceanDNA-a4364/markers.fasta -db /var/lib/cwl/stgb9cf194e-abe6-43fc-902f-74b4c9eaa0b8/dqc_reference/reference_markers.fasta -out OceanDNA-a4364/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:13,315] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:13,315] [INFO] Selected 0 target genomes.
[2023-03-16 04:54:13,315] [INFO] Target genome list was writen to OceanDNA-a4364/target_genomes.txt
[2023-03-16 04:54:13,315] [ERROR] File is empty. [OceanDNA-a4364/target_genomes.txt]
[2023-03-16 04:54:13,316] [ERROR] Task failed. No target genome found.
[2023-03-16 04:54:13,316] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:13,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9cf194e-abe6-43fc-902f-74b4c9eaa0b8/dqc_reference/checkm_data
[2023-03-16 04:54:13,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:13,329] [INFO] Task started: CheckM
[2023-03-16 04:54:13,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4364/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4364/checkm_input OceanDNA-a4364/checkm_result
[2023-03-16 04:54:31,897] [INFO] Task succeeded: CheckM
[2023-03-16 04:54:31,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.33%
Contamintation: 2.93%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 04:54:31,899] [INFO] ===== Completeness check finished =====
[2023-03-16 04:54:31,899] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:54:31,899] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4364/markers.fasta)
[2023-03-16 04:54:31,899] [INFO] Task started: Blastn
[2023-03-16 04:54:31,899] [INFO] Running command: blastn -query OceanDNA-a4364/markers.fasta -db /var/lib/cwl/stgb9cf194e-abe6-43fc-902f-74b4c9eaa0b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4364/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:32,394] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:32,395] [INFO] Selected 5 target genomes.
[2023-03-16 04:54:32,395] [INFO] Target genome list was writen to OceanDNA-a4364/target_genomes_gtdb.txt
[2023-03-16 04:54:32,402] [INFO] Task started: fastANI
[2023-03-16 04:54:32,402] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc0c86ec-631f-4dd7-8be9-2c8291e28764/OceanDNA-a4364.fa --refList OceanDNA-a4364/target_genomes_gtdb.txt --output OceanDNA-a4364/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:54:33,400] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:33,402] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:54:33,402] [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_002506755.1	s__MGIIb-O3 sp002506755	99.6468	174	205	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.90	99.90	0.92	0.92	2	conclusive
--------------------------------------------------------------------------------
[2023-03-16 04:54:33,402] [INFO] GTDB search result was written to OceanDNA-a4364/result_gtdb.tsv
[2023-03-16 04:54:33,402] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:54:33,403] [INFO] DFAST_QC result json was written to OceanDNA-a4364/dqc_result.json
[2023-03-16 04:54:33,403] [INFO] DFAST_QC completed!
[2023-03-16 04:54:33,403] [INFO] Total running time: 0h0m26s