[2023-03-17 15:09:40,842] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:09:40,843] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:09:40,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ccf366d-d7b7-47e9-8f62-4622fc47f815/dqc_reference
[2023-03-17 15:09:42,329] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:09:42,329] [INFO] Task started: Prodigal
[2023-03-17 15:09:42,329] [INFO] Running command: cat /var/lib/cwl/stge0e3185c-b43d-4df8-8076-2a6976a1a7e4/OceanDNA-a1.fa | prodigal -d OceanDNA-a1/cds.fna -a OceanDNA-a1/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:09:47,734] [INFO] Task succeeded: Prodigal
[2023-03-17 15:09:47,735] [INFO] Task started: HMMsearch
[2023-03-17 15:09:47,735] [INFO] Running command: hmmsearch --tblout OceanDNA-a1/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ccf366d-d7b7-47e9-8f62-4622fc47f815/dqc_reference/reference_markers.hmm OceanDNA-a1/protein.faa > /dev/null
[2023-03-17 15:09:48,038] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:09:48,039] [WARNING] Found 1/6 markers. [/var/lib/cwl/stge0e3185c-b43d-4df8-8076-2a6976a1a7e4/OceanDNA-a1.fa]
[2023-03-17 15:09:48,043] [INFO] Query marker FASTA was written to OceanDNA-a1/markers.fasta
[2023-03-17 15:09:48,045] [INFO] Task started: Blastn
[2023-03-17 15:09:48,045] [INFO] Running command: blastn -query OceanDNA-a1/markers.fasta -db /var/lib/cwl/stg8ccf366d-d7b7-47e9-8f62-4622fc47f815/dqc_reference/reference_markers.fasta -out OceanDNA-a1/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:09:49,164] [INFO] Task succeeded: Blastn
[2023-03-17 15:09:49,165] [INFO] Selected 0 target genomes.
[2023-03-17 15:09:49,165] [INFO] Target genome list was writen to OceanDNA-a1/target_genomes.txt
[2023-03-17 15:09:49,165] [ERROR] File is empty. [OceanDNA-a1/target_genomes.txt]
[2023-03-17 15:09:49,165] [ERROR] Task failed. No target genome found.
[2023-03-17 15:09:49,165] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:09:49,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ccf366d-d7b7-47e9-8f62-4622fc47f815/dqc_reference/checkm_data
[2023-03-17 15:09:49,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:09:49,221] [INFO] Task started: CheckM
[2023-03-17 15:09:49,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1/checkm_input OceanDNA-a1/checkm_result
[2023-03-17 15:10:06,906] [INFO] Task succeeded: CheckM
[2023-03-17 15:10:06,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 15:10:06,908] [INFO] ===== Completeness check finished =====
[2023-03-17 15:10:06,908] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:10:06,908] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1/markers.fasta)
[2023-03-17 15:10:06,910] [INFO] Task started: Blastn
[2023-03-17 15:10:06,910] [INFO] Running command: blastn -query OceanDNA-a1/markers.fasta -db /var/lib/cwl/stg8ccf366d-d7b7-47e9-8f62-4622fc47f815/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:10:07,631] [INFO] Task succeeded: Blastn
[2023-03-17 15:10:07,631] [INFO] Selected 2 target genomes.
[2023-03-17 15:10:07,631] [INFO] Target genome list was writen to OceanDNA-a1/target_genomes_gtdb.txt
[2023-03-17 15:10:07,718] [INFO] Task started: fastANI
[2023-03-17 15:10:07,718] [INFO] Running command: fastANI --query /var/lib/cwl/stge0e3185c-b43d-4df8-8076-2a6976a1a7e4/OceanDNA-a1.fa --refList OceanDNA-a1/target_genomes_gtdb.txt --output OceanDNA-a1/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:10:08,208] [INFO] Task succeeded: fastANI
[2023-03-17 15:10:08,210] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 15:10:08,210] [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_002688965.1	s__GCA-2688965 sp002688965	99.8571	120	135	d__Archaea;p__Aenigmatarchaeota;c__Aenigmatarchaeia;o__GW2011-AR5;f__GCA-2688965;g__GCA-2688965	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-17 15:10:08,211] [INFO] GTDB search result was written to OceanDNA-a1/result_gtdb.tsv
[2023-03-17 15:10:08,211] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:10:08,211] [INFO] DFAST_QC result json was written to OceanDNA-a1/dqc_result.json
[2023-03-17 15:10:08,211] [INFO] DFAST_QC completed!
[2023-03-17 15:10:08,211] [INFO] Total running time: 0h0m27s