[2023-03-16 11:50:51,438] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:50:51,438] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:50:51,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg70f9a498-d154-40cf-adbf-7b8d9cc3c706/dqc_reference
[2023-03-16 11:50:54,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:50:54,326] [INFO] Task started: Prodigal
[2023-03-16 11:50:54,327] [INFO] Running command: cat /var/lib/cwl/stg047f4c4b-eb98-4704-af0d-8b6d28df6bc1/OceanDNA-a5198.fa | prodigal -d OceanDNA-a5198/cds.fna -a OceanDNA-a5198/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:50:58,237] [INFO] Task succeeded: Prodigal
[2023-03-16 11:50:58,237] [INFO] Task started: HMMsearch
[2023-03-16 11:50:58,237] [INFO] Running command: hmmsearch --tblout OceanDNA-a5198/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70f9a498-d154-40cf-adbf-7b8d9cc3c706/dqc_reference/reference_markers.hmm OceanDNA-a5198/protein.faa > /dev/null
[2023-03-16 11:50:58,344] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:50:58,345] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg047f4c4b-eb98-4704-af0d-8b6d28df6bc1/OceanDNA-a5198.fa]
[2023-03-16 11:50:58,351] [INFO] Query marker FASTA was written to OceanDNA-a5198/markers.fasta
[2023-03-16 11:50:58,351] [INFO] Task started: Blastn
[2023-03-16 11:50:58,351] [INFO] Running command: blastn -query OceanDNA-a5198/markers.fasta -db /var/lib/cwl/stg70f9a498-d154-40cf-adbf-7b8d9cc3c706/dqc_reference/reference_markers.fasta -out OceanDNA-a5198/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:50:58,850] [INFO] Task succeeded: Blastn
[2023-03-16 11:50:58,851] [INFO] Selected 0 target genomes.
[2023-03-16 11:50:58,851] [INFO] Target genome list was writen to OceanDNA-a5198/target_genomes.txt
[2023-03-16 11:50:58,851] [ERROR] File is empty. [OceanDNA-a5198/target_genomes.txt]
[2023-03-16 11:50:58,851] [ERROR] Task failed. No target genome found.
[2023-03-16 11:50:58,851] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:50:58,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70f9a498-d154-40cf-adbf-7b8d9cc3c706/dqc_reference/checkm_data
[2023-03-16 11:50:58,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:50:58,908] [INFO] Task started: CheckM
[2023-03-16 11:50:58,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5198/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5198/checkm_input OceanDNA-a5198/checkm_result
[2023-03-16 11:51:17,353] [INFO] Task succeeded: CheckM
[2023-03-16 11:51:17,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:51:17,354] [INFO] ===== Completeness check finished =====
[2023-03-16 11:51:17,354] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:51:17,355] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5198/markers.fasta)
[2023-03-16 11:51:17,355] [INFO] Task started: Blastn
[2023-03-16 11:51:17,355] [INFO] Running command: blastn -query OceanDNA-a5198/markers.fasta -db /var/lib/cwl/stg70f9a498-d154-40cf-adbf-7b8d9cc3c706/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5198/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:51:17,850] [INFO] Task succeeded: Blastn
[2023-03-16 11:51:17,850] [INFO] Selected 2 target genomes.
[2023-03-16 11:51:17,850] [INFO] Target genome list was writen to OceanDNA-a5198/target_genomes_gtdb.txt
[2023-03-16 11:51:17,968] [INFO] Task started: fastANI
[2023-03-16 11:51:17,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg047f4c4b-eb98-4704-af0d-8b6d28df6bc1/OceanDNA-a5198.fa --refList OceanDNA-a5198/target_genomes_gtdb.txt --output OceanDNA-a5198/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:51:18,393] [INFO] Task succeeded: fastANI
[2023-03-16 11:51:18,395] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:51:18,395] [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_002502135.1	s__UBA543 sp002502135	99.7668	208	225	d__Archaea;p__Undinarchaeota;c__Undinarchaeia;o__Undinarchaeales;f__UBA543;g__UBA543	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-16 11:51:18,395] [INFO] GTDB search result was written to OceanDNA-a5198/result_gtdb.tsv
[2023-03-16 11:51:18,395] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:51:18,396] [INFO] DFAST_QC result json was written to OceanDNA-a5198/dqc_result.json
[2023-03-16 11:51:18,396] [INFO] DFAST_QC completed!
[2023-03-16 11:51:18,396] [INFO] Total running time: 0h0m27s