[2023-03-16 07:49:28,793] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:49:28,794] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:49:28,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c67ab05-6082-4641-a8e8-8603d0012e9b/dqc_reference
[2023-03-16 07:49:29,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:49:29,913] [INFO] Task started: Prodigal
[2023-03-16 07:49:29,913] [INFO] Running command: cat /var/lib/cwl/stg7eb3fb1d-13ae-4c02-9e19-d2545327f04d/OceanDNA-b13172.fa | prodigal -d OceanDNA-b13172/cds.fna -a OceanDNA-b13172/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:49:40,940] [INFO] Task succeeded: Prodigal
[2023-03-16 07:49:40,941] [INFO] Task started: HMMsearch
[2023-03-16 07:49:40,941] [INFO] Running command: hmmsearch --tblout OceanDNA-b13172/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c67ab05-6082-4641-a8e8-8603d0012e9b/dqc_reference/reference_markers.hmm OceanDNA-b13172/protein.faa > /dev/null
[2023-03-16 07:49:41,127] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:49:41,127] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7eb3fb1d-13ae-4c02-9e19-d2545327f04d/OceanDNA-b13172.fa]
[2023-03-16 07:49:41,145] [INFO] Query marker FASTA was written to OceanDNA-b13172/markers.fasta
[2023-03-16 07:49:41,146] [INFO] Task started: Blastn
[2023-03-16 07:49:41,146] [INFO] Running command: blastn -query OceanDNA-b13172/markers.fasta -db /var/lib/cwl/stg7c67ab05-6082-4641-a8e8-8603d0012e9b/dqc_reference/reference_markers.fasta -out OceanDNA-b13172/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:49:41,655] [INFO] Task succeeded: Blastn
[2023-03-16 07:49:41,664] [INFO] Selected 24 target genomes.
[2023-03-16 07:49:41,665] [INFO] Target genome list was writen to OceanDNA-b13172/target_genomes.txt
[2023-03-16 07:49:41,704] [INFO] Task started: fastANI
[2023-03-16 07:49:41,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eb3fb1d-13ae-4c02-9e19-d2545327f04d/OceanDNA-b13172.fa --refList OceanDNA-b13172/target_genomes.txt --output OceanDNA-b13172/fastani_result.tsv --threads 1
[2023-03-16 07:49:54,575] [INFO] Task succeeded: fastANI
[2023-03-16 07:49:54,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c67ab05-6082-4641-a8e8-8603d0012e9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:49:54,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c67ab05-6082-4641-a8e8-8603d0012e9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:49:54,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:49:54,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:49:54,576] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-16 07:49:54,577] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13172/tc_result.tsv
[2023-03-16 07:49:54,577] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:49:54,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:49:54,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c67ab05-6082-4641-a8e8-8603d0012e9b/dqc_reference/checkm_data
[2023-03-16 07:49:54,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:49:54,586] [INFO] Task started: CheckM
[2023-03-16 07:49:54,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13172/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13172/checkm_input OceanDNA-b13172/checkm_result
[2023-03-16 07:50:25,998] [INFO] Task succeeded: CheckM
[2023-03-16 07:50:25,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:50:26,014] [INFO] ===== Completeness check finished =====
[2023-03-16 07:50:26,015] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:50:26,015] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13172/markers.fasta)
[2023-03-16 07:50:26,016] [INFO] Task started: Blastn
[2023-03-16 07:50:26,016] [INFO] Running command: blastn -query OceanDNA-b13172/markers.fasta -db /var/lib/cwl/stg7c67ab05-6082-4641-a8e8-8603d0012e9b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13172/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:50:26,689] [INFO] Task succeeded: Blastn
[2023-03-16 07:50:26,691] [INFO] Selected 20 target genomes.
[2023-03-16 07:50:26,691] [INFO] Target genome list was writen to OceanDNA-b13172/target_genomes_gtdb.txt
[2023-03-16 07:50:26,826] [INFO] Task started: fastANI
[2023-03-16 07:50:26,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eb3fb1d-13ae-4c02-9e19-d2545327f04d/OceanDNA-b13172.fa --refList OceanDNA-b13172/target_genomes_gtdb.txt --output OceanDNA-b13172/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:50:36,925] [INFO] Task succeeded: fastANI
[2023-03-16 07:50:36,927] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:50:36,927] [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_002716825.1	s__UBA4207 sp002716825	85.213	455	661	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA4207	95.0	99.84	99.84	0.97	0.97	2	-
GCA_002787775.1	s__UBA4207 sp002787775	78.5613	241	661	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA4207	95.0	99.91	99.91	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-16 07:50:36,927] [INFO] GTDB search result was written to OceanDNA-b13172/result_gtdb.tsv
[2023-03-16 07:50:36,927] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:50:36,928] [INFO] DFAST_QC result json was written to OceanDNA-b13172/dqc_result.json
[2023-03-16 07:50:36,929] [INFO] DFAST_QC completed!
[2023-03-16 07:50:36,929] [INFO] Total running time: 0h1m8s