[2023-03-14 11:49:37,368] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:37,369] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:37,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg8dcb96a7-1cc1-4398-baf0-b5a85945aeed/dqc_reference
[2023-03-14 11:49:38,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:38,963] [INFO] Task started: Prodigal
[2023-03-14 11:49:38,963] [INFO] Running command: cat /var/lib/cwl/stg14b82316-5406-49b8-87f5-3d61ec7c4709/OceanDNA-a1025.fa | prodigal -d OceanDNA-a1025/cds.fna -a OceanDNA-a1025/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:49:42,955] [INFO] Task succeeded: Prodigal
[2023-03-14 11:49:42,955] [INFO] Task started: HMMsearch
[2023-03-14 11:49:42,955] [INFO] Running command: hmmsearch --tblout OceanDNA-a1025/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8dcb96a7-1cc1-4398-baf0-b5a85945aeed/dqc_reference/reference_markers.hmm OceanDNA-a1025/protein.faa > /dev/null
[2023-03-14 11:49:43,072] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:49:43,073] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg14b82316-5406-49b8-87f5-3d61ec7c4709/OceanDNA-a1025.fa]
[2023-03-14 11:49:43,088] [INFO] Query marker FASTA was written to OceanDNA-a1025/markers.fasta
[2023-03-14 11:49:43,088] [INFO] Task started: Blastn
[2023-03-14 11:49:43,089] [INFO] Running command: blastn -query OceanDNA-a1025/markers.fasta -db /var/lib/cwl/stg8dcb96a7-1cc1-4398-baf0-b5a85945aeed/dqc_reference/reference_markers.fasta -out OceanDNA-a1025/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:49:44,086] [INFO] Task succeeded: Blastn
[2023-03-14 11:49:44,102] [INFO] Selected 0 target genomes.
[2023-03-14 11:49:44,103] [INFO] Target genome list was writen to OceanDNA-a1025/target_genomes.txt
[2023-03-14 11:49:44,103] [ERROR] File is empty. [OceanDNA-a1025/target_genomes.txt]
[2023-03-14 11:49:44,103] [ERROR] Task failed. No target genome found.
[2023-03-14 11:49:44,103] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:49:44,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8dcb96a7-1cc1-4398-baf0-b5a85945aeed/dqc_reference/checkm_data
[2023-03-14 11:49:44,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:49:44,123] [INFO] Task started: CheckM
[2023-03-14 11:49:44,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1025/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1025/checkm_input OceanDNA-a1025/checkm_result
[2023-03-14 11:50:01,661] [INFO] Task succeeded: CheckM
[2023-03-14 11:50:01,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 11:50:01,718] [INFO] ===== Completeness check finished =====
[2023-03-14 11:50:01,718] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:50:01,718] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1025/markers.fasta)
[2023-03-14 11:50:01,718] [INFO] Task started: Blastn
[2023-03-14 11:50:01,718] [INFO] Running command: blastn -query OceanDNA-a1025/markers.fasta -db /var/lib/cwl/stg8dcb96a7-1cc1-4398-baf0-b5a85945aeed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1025/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:50:02,320] [INFO] Task succeeded: Blastn
[2023-03-14 11:50:02,326] [INFO] Selected 1 target genomes.
[2023-03-14 11:50:02,326] [INFO] Target genome list was writen to OceanDNA-a1025/target_genomes_gtdb.txt
[2023-03-14 11:50:02,329] [INFO] Task started: fastANI
[2023-03-14 11:50:02,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg14b82316-5406-49b8-87f5-3d61ec7c4709/OceanDNA-a1025.fa --refList OceanDNA-a1025/target_genomes_gtdb.txt --output OceanDNA-a1025/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:50:02,514] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:02,516] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:50:02,516] [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_002687735.1	s__UBA493 sp002687735	99.8885	151	239	d__Archaea;p__Iainarchaeota;c__Iainarchaeia;o__Iainarchaeales;f__Iainarchaeaceae;g__UBA493	95.0	99.60	99.60	0.62	0.62	2	conclusive
--------------------------------------------------------------------------------
[2023-03-14 11:50:02,518] [INFO] GTDB search result was written to OceanDNA-a1025/result_gtdb.tsv
[2023-03-14 11:50:02,523] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:50:02,527] [INFO] DFAST_QC result json was written to OceanDNA-a1025/dqc_result.json
[2023-03-14 11:50:02,527] [INFO] DFAST_QC completed!
[2023-03-14 11:50:02,527] [INFO] Total running time: 0h0m25s