[2023-03-16 18:28:42,337] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:28:42,337] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:28:42,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg11f768a9-58dd-4b6a-b3c5-f4583430f56e/dqc_reference
[2023-03-16 18:28:43,488] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:28:43,488] [INFO] Task started: Prodigal
[2023-03-16 18:28:43,489] [INFO] Running command: cat /var/lib/cwl/stga6af4a49-2732-4c26-8348-8e76ba840fcb/OceanDNA-a5201.fa | prodigal -d OceanDNA-a5201/cds.fna -a OceanDNA-a5201/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:28:47,089] [INFO] Task succeeded: Prodigal
[2023-03-16 18:28:47,090] [INFO] Task started: HMMsearch
[2023-03-16 18:28:47,090] [INFO] Running command: hmmsearch --tblout OceanDNA-a5201/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11f768a9-58dd-4b6a-b3c5-f4583430f56e/dqc_reference/reference_markers.hmm OceanDNA-a5201/protein.faa > /dev/null
[2023-03-16 18:28:47,218] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:28:47,218] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga6af4a49-2732-4c26-8348-8e76ba840fcb/OceanDNA-a5201.fa]
[2023-03-16 18:28:47,279] [INFO] Query marker FASTA was written to OceanDNA-a5201/markers.fasta
[2023-03-16 18:28:47,282] [INFO] Task started: Blastn
[2023-03-16 18:28:47,283] [INFO] Running command: blastn -query OceanDNA-a5201/markers.fasta -db /var/lib/cwl/stg11f768a9-58dd-4b6a-b3c5-f4583430f56e/dqc_reference/reference_markers.fasta -out OceanDNA-a5201/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:28:47,927] [INFO] Task succeeded: Blastn
[2023-03-16 18:28:47,928] [INFO] Selected 0 target genomes.
[2023-03-16 18:28:47,928] [INFO] Target genome list was writen to OceanDNA-a5201/target_genomes.txt
[2023-03-16 18:28:47,928] [ERROR] File is empty. [OceanDNA-a5201/target_genomes.txt]
[2023-03-16 18:28:47,928] [ERROR] Task failed. No target genome found.
[2023-03-16 18:28:47,929] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:28:47,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11f768a9-58dd-4b6a-b3c5-f4583430f56e/dqc_reference/checkm_data
[2023-03-16 18:28:47,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:28:47,941] [INFO] Task started: CheckM
[2023-03-16 18:28:47,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5201/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5201/checkm_input OceanDNA-a5201/checkm_result
[2023-03-16 18:29:10,874] [INFO] Task succeeded: CheckM
[2023-03-16 18:29:10,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:29:10,876] [INFO] ===== Completeness check finished =====
[2023-03-16 18:29:10,876] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:29:10,876] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5201/markers.fasta)
[2023-03-16 18:29:10,879] [INFO] Task started: Blastn
[2023-03-16 18:29:10,879] [INFO] Running command: blastn -query OceanDNA-a5201/markers.fasta -db /var/lib/cwl/stg11f768a9-58dd-4b6a-b3c5-f4583430f56e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5201/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:29:11,433] [INFO] Task succeeded: Blastn
[2023-03-16 18:29:11,434] [INFO] Selected 3 target genomes.
[2023-03-16 18:29:11,434] [INFO] Target genome list was writen to OceanDNA-a5201/target_genomes_gtdb.txt
[2023-03-16 18:29:11,439] [INFO] Task started: fastANI
[2023-03-16 18:29:11,439] [INFO] Running command: fastANI --query /var/lib/cwl/stga6af4a49-2732-4c26-8348-8e76ba840fcb/OceanDNA-a5201.fa --refList OceanDNA-a5201/target_genomes_gtdb.txt --output OceanDNA-a5201/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:29:11,864] [INFO] Task succeeded: fastANI
[2023-03-16 18:29:11,867] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:29:11,867] [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_002495465.1	s__Undinarchaeum marinum	96.6219	141	155	d__Archaea;p__Undinarchaeota;c__Undinarchaeia;o__Undinarchaeales;f__Undinarchaeaceae;g__Undinarchaeum	95.0	96.77	96.77	0.92	0.92	2	conclusive
GCA_014189675.1	s__Undinarchaeum sp014189675	93.9278	141	155	d__Archaea;p__Undinarchaeota;c__Undinarchaeia;o__Undinarchaeales;f__Undinarchaeaceae;g__Undinarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687935.1	s__Undinarchaeum sp002687935	85.0711	141	155	d__Archaea;p__Undinarchaeota;c__Undinarchaeia;o__Undinarchaeales;f__Undinarchaeaceae;g__Undinarchaeum	95.0	99.93	99.89	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2023-03-16 18:29:11,867] [INFO] GTDB search result was written to OceanDNA-a5201/result_gtdb.tsv
[2023-03-16 18:29:11,867] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:29:11,868] [INFO] DFAST_QC result json was written to OceanDNA-a5201/dqc_result.json
[2023-03-16 18:29:11,868] [INFO] DFAST_QC completed!
[2023-03-16 18:29:11,868] [INFO] Total running time: 0h0m30s