[2023-03-19 01:50:01,527] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,528] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,528] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6f31f34-3917-4e91-aead-12a76fe8043e/dqc_reference
[2023-03-19 01:50:02,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,653] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,653] [INFO] Running command: cat /var/lib/cwl/stg4442ef14-c5f0-4504-825b-0217d36d74d8/OceanDNA-a991.fa | prodigal -d OceanDNA-a991/cds.fna -a OceanDNA-a991/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:08,835] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:08,835] [INFO] Task started: HMMsearch
[2023-03-19 01:50:08,835] [INFO] Running command: hmmsearch --tblout OceanDNA-a991/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6f31f34-3917-4e91-aead-12a76fe8043e/dqc_reference/reference_markers.hmm OceanDNA-a991/protein.faa > /dev/null
[2023-03-19 01:50:08,957] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:08,958] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg4442ef14-c5f0-4504-825b-0217d36d74d8/OceanDNA-a991.fa]
[2023-03-19 01:50:08,966] [INFO] Query marker FASTA was written to OceanDNA-a991/markers.fasta
[2023-03-19 01:50:08,967] [INFO] Task started: Blastn
[2023-03-19 01:50:08,967] [INFO] Running command: blastn -query OceanDNA-a991/markers.fasta -db /var/lib/cwl/stgd6f31f34-3917-4e91-aead-12a76fe8043e/dqc_reference/reference_markers.fasta -out OceanDNA-a991/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:09,372] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:09,373] [INFO] Selected 0 target genomes.
[2023-03-19 01:50:09,373] [INFO] Target genome list was writen to OceanDNA-a991/target_genomes.txt
[2023-03-19 01:50:09,373] [ERROR] File is empty. [OceanDNA-a991/target_genomes.txt]
[2023-03-19 01:50:09,373] [ERROR] Task failed. No target genome found.
[2023-03-19 01:50:09,373] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:09,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6f31f34-3917-4e91-aead-12a76fe8043e/dqc_reference/checkm_data
[2023-03-19 01:50:09,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:09,434] [INFO] Task started: CheckM
[2023-03-19 01:50:09,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a991/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a991/checkm_input OceanDNA-a991/checkm_result
[2023-03-19 01:50:32,284] [INFO] Task succeeded: CheckM
[2023-03-19 01:50:32,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:50:32,286] [INFO] ===== Completeness check finished =====
[2023-03-19 01:50:32,286] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:50:32,286] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a991/markers.fasta)
[2023-03-19 01:50:32,287] [INFO] Task started: Blastn
[2023-03-19 01:50:32,287] [INFO] Running command: blastn -query OceanDNA-a991/markers.fasta -db /var/lib/cwl/stgd6f31f34-3917-4e91-aead-12a76fe8043e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a991/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:32,996] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:32,997] [INFO] Selected 2 target genomes.
[2023-03-19 01:50:32,997] [INFO] Target genome list was writen to OceanDNA-a991/target_genomes_gtdb.txt
[2023-03-19 01:50:32,999] [INFO] Task started: fastANI
[2023-03-19 01:50:32,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg4442ef14-c5f0-4504-825b-0217d36d74d8/OceanDNA-a991.fa --refList OceanDNA-a991/target_genomes_gtdb.txt --output OceanDNA-a991/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:50:33,464] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:33,466] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:50:33,466] [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_002503845.1	s__UBA12382 sp002503845	92.2094	249	269	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__UBA12382;g__UBA12382	95.0	99.52	97.09	0.98	0.96	8	-
GCA_009889685.1	s__UBA12382 sp009889685	83.0264	159	269	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__UBA12382;g__UBA12382	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:50:33,467] [INFO] GTDB search result was written to OceanDNA-a991/result_gtdb.tsv
[2023-03-19 01:50:33,467] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:50:33,468] [INFO] DFAST_QC result json was written to OceanDNA-a991/dqc_result.json
[2023-03-19 01:50:33,468] [INFO] DFAST_QC completed!
[2023-03-19 01:50:33,468] [INFO] Total running time: 0h0m32s