[2023-03-18 21:29:07,952] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:29:07,952] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:29:07,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg587021f4-9f4b-4fa4-ba89-72b9f332f5e0/dqc_reference
[2023-03-18 21:29:09,063] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:29:09,064] [INFO] Task started: Prodigal
[2023-03-18 21:29:09,064] [INFO] Running command: cat /var/lib/cwl/stgd6c8ef6c-0b2a-4c54-bdc9-4cae61b98621/OceanDNA-a1301.fa | prodigal -d OceanDNA-a1301/cds.fna -a OceanDNA-a1301/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:29:10,607] [INFO] Task succeeded: Prodigal
[2023-03-18 21:29:10,608] [INFO] Task started: HMMsearch
[2023-03-18 21:29:10,608] [INFO] Running command: hmmsearch --tblout OceanDNA-a1301/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg587021f4-9f4b-4fa4-ba89-72b9f332f5e0/dqc_reference/reference_markers.hmm OceanDNA-a1301/protein.faa > /dev/null
[2023-03-18 21:29:10,702] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:29:10,703] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd6c8ef6c-0b2a-4c54-bdc9-4cae61b98621/OceanDNA-a1301.fa]
[2023-03-18 21:29:10,706] [INFO] Query marker FASTA was written to OceanDNA-a1301/markers.fasta
[2023-03-18 21:29:10,708] [INFO] Task started: Blastn
[2023-03-18 21:29:10,708] [INFO] Running command: blastn -query OceanDNA-a1301/markers.fasta -db /var/lib/cwl/stg587021f4-9f4b-4fa4-ba89-72b9f332f5e0/dqc_reference/reference_markers.fasta -out OceanDNA-a1301/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:11,160] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:11,160] [INFO] Selected 0 target genomes.
[2023-03-18 21:29:11,161] [INFO] Target genome list was writen to OceanDNA-a1301/target_genomes.txt
[2023-03-18 21:29:11,161] [ERROR] File is empty. [OceanDNA-a1301/target_genomes.txt]
[2023-03-18 21:29:11,161] [ERROR] Task failed. No target genome found.
[2023-03-18 21:29:11,161] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:29:11,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg587021f4-9f4b-4fa4-ba89-72b9f332f5e0/dqc_reference/checkm_data
[2023-03-18 21:29:11,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:29:11,217] [INFO] Task started: CheckM
[2023-03-18 21:29:11,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1301/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1301/checkm_input OceanDNA-a1301/checkm_result
[2023-03-18 21:29:23,028] [INFO] Task succeeded: CheckM
[2023-03-18 21:29:23,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:29:23,029] [INFO] ===== Completeness check finished =====
[2023-03-18 21:29:23,029] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:29:23,029] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1301/markers.fasta)
[2023-03-18 21:29:23,031] [INFO] Task started: Blastn
[2023-03-18 21:29:23,031] [INFO] Running command: blastn -query OceanDNA-a1301/markers.fasta -db /var/lib/cwl/stg587021f4-9f4b-4fa4-ba89-72b9f332f5e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1301/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:23,702] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:23,703] [INFO] Selected 5 target genomes.
[2023-03-18 21:29:23,703] [INFO] Target genome list was writen to OceanDNA-a1301/target_genomes_gtdb.txt
[2023-03-18 21:29:23,705] [INFO] Task started: fastANI
[2023-03-18 21:29:23,706] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6c8ef6c-0b2a-4c54-bdc9-4cae61b98621/OceanDNA-a1301.fa --refList OceanDNA-a1301/target_genomes_gtdb.txt --output OceanDNA-a1301/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:29:24,669] [INFO] Task succeeded: fastANI
[2023-03-18 21:29:24,671] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:29:24,671] [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_014239585.1	s__ARS21 sp014239585	83.3279	85	95	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__UBA10117;f__ARS21;g__ARS21	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:29:24,671] [INFO] GTDB search result was written to OceanDNA-a1301/result_gtdb.tsv
[2023-03-18 21:29:24,671] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:29:24,672] [INFO] DFAST_QC result json was written to OceanDNA-a1301/dqc_result.json
[2023-03-18 21:29:24,672] [INFO] DFAST_QC completed!
[2023-03-18 21:29:24,672] [INFO] Total running time: 0h0m17s