[2023-03-18 07:29:29,821] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:29,821] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:29,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg08ab2b45-d39e-473c-9b24-6cdb7c310f9c/dqc_reference
[2023-03-18 07:29:30,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:30,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:30,935] [INFO] Running command: cat /var/lib/cwl/stgb2f944c0-62b3-4d55-a472-670194a77b0f/OceanDNA-a1730.fa | prodigal -d OceanDNA-a1730/cds.fna -a OceanDNA-a1730/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:32,934] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:32,934] [INFO] Task started: HMMsearch
[2023-03-18 07:29:32,934] [INFO] Running command: hmmsearch --tblout OceanDNA-a1730/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08ab2b45-d39e-473c-9b24-6cdb7c310f9c/dqc_reference/reference_markers.hmm OceanDNA-a1730/protein.faa > /dev/null
[2023-03-18 07:29:33,073] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:33,074] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb2f944c0-62b3-4d55-a472-670194a77b0f/OceanDNA-a1730.fa]
[2023-03-18 07:29:33,079] [INFO] Query marker FASTA was written to OceanDNA-a1730/markers.fasta
[2023-03-18 07:29:33,081] [INFO] Task started: Blastn
[2023-03-18 07:29:33,081] [INFO] Running command: blastn -query OceanDNA-a1730/markers.fasta -db /var/lib/cwl/stg08ab2b45-d39e-473c-9b24-6cdb7c310f9c/dqc_reference/reference_markers.fasta -out OceanDNA-a1730/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:33,602] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:33,603] [INFO] Selected 0 target genomes.
[2023-03-18 07:29:33,603] [INFO] Target genome list was writen to OceanDNA-a1730/target_genomes.txt
[2023-03-18 07:29:33,603] [ERROR] File is empty. [OceanDNA-a1730/target_genomes.txt]
[2023-03-18 07:29:33,603] [ERROR] Task failed. No target genome found.
[2023-03-18 07:29:33,603] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:33,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08ab2b45-d39e-473c-9b24-6cdb7c310f9c/dqc_reference/checkm_data
[2023-03-18 07:29:33,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:33,653] [INFO] Task started: CheckM
[2023-03-18 07:29:33,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1730/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1730/checkm_input OceanDNA-a1730/checkm_result
[2023-03-18 07:29:50,032] [INFO] Task succeeded: CheckM
[2023-03-18 07:29:50,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:29:50,034] [INFO] ===== Completeness check finished =====
[2023-03-18 07:29:50,034] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:29:50,034] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1730/markers.fasta)
[2023-03-18 07:29:50,036] [INFO] Task started: Blastn
[2023-03-18 07:29:50,036] [INFO] Running command: blastn -query OceanDNA-a1730/markers.fasta -db /var/lib/cwl/stg08ab2b45-d39e-473c-9b24-6cdb7c310f9c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1730/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:50,846] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:50,847] [INFO] Selected 5 target genomes.
[2023-03-18 07:29:50,847] [INFO] Target genome list was writen to OceanDNA-a1730/target_genomes_gtdb.txt
[2023-03-18 07:29:50,976] [INFO] Task started: fastANI
[2023-03-18 07:29:50,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2f944c0-62b3-4d55-a472-670194a77b0f/OceanDNA-a1730.fa --refList OceanDNA-a1730/target_genomes_gtdb.txt --output OceanDNA-a1730/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:29:51,725] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:51,728] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:29:51,728] [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_002731905.1	s__UBA8886 sp002731905	91.141	60	71	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687355.1	s__UBA8886 sp002687355	91.1203	50	71	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	99.48	99.48	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:29:51,728] [INFO] GTDB search result was written to OceanDNA-a1730/result_gtdb.tsv
[2023-03-18 07:29:51,728] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:29:51,729] [INFO] DFAST_QC result json was written to OceanDNA-a1730/dqc_result.json
[2023-03-18 07:29:51,729] [INFO] DFAST_QC completed!
[2023-03-18 07:29:51,729] [INFO] Total running time: 0h0m22s