[2023-03-18 08:17:17,688] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,688] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg7df71b2f-9838-4268-8427-a1135ceeb0ef/dqc_reference
[2023-03-18 08:17:18,942] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stg8fb34425-83d6-4afd-8981-c40952ba1ba6/OceanDNA-b32483.fa | prodigal -d OceanDNA-b32483/cds.fna -a OceanDNA-b32483/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:21,608] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:21,608] [INFO] Task started: HMMsearch
[2023-03-18 08:17:21,608] [INFO] Running command: hmmsearch --tblout OceanDNA-b32483/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7df71b2f-9838-4268-8427-a1135ceeb0ef/dqc_reference/reference_markers.hmm OceanDNA-b32483/protein.faa > /dev/null
[2023-03-18 08:17:21,781] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:21,782] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8fb34425-83d6-4afd-8981-c40952ba1ba6/OceanDNA-b32483.fa]
[2023-03-18 08:17:21,790] [INFO] Query marker FASTA was written to OceanDNA-b32483/markers.fasta
[2023-03-18 08:17:21,792] [INFO] Task started: Blastn
[2023-03-18 08:17:21,792] [INFO] Running command: blastn -query OceanDNA-b32483/markers.fasta -db /var/lib/cwl/stg7df71b2f-9838-4268-8427-a1135ceeb0ef/dqc_reference/reference_markers.fasta -out OceanDNA-b32483/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:22,471] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:22,472] [INFO] Selected 9 target genomes.
[2023-03-18 08:17:22,472] [INFO] Target genome list was writen to OceanDNA-b32483/target_genomes.txt
[2023-03-18 08:17:22,477] [INFO] Task started: fastANI
[2023-03-18 08:17:22,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fb34425-83d6-4afd-8981-c40952ba1ba6/OceanDNA-b32483.fa --refList OceanDNA-b32483/target_genomes.txt --output OceanDNA-b32483/fastani_result.tsv --threads 1
[2023-03-18 08:17:25,862] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:25,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7df71b2f-9838-4268-8427-a1135ceeb0ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:25,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7df71b2f-9838-4268-8427-a1135ceeb0ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:25,862] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:25,863] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:25,863] [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
--------------------------------------------------------------------------------
[2023-03-18 08:17:25,863] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32483/tc_result.tsv
[2023-03-18 08:17:25,863] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:25,863] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:25,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7df71b2f-9838-4268-8427-a1135ceeb0ef/dqc_reference/checkm_data
[2023-03-18 08:17:25,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:25,867] [INFO] Task started: CheckM
[2023-03-18 08:17:25,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32483/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32483/checkm_input OceanDNA-b32483/checkm_result
[2023-03-18 08:17:42,745] [INFO] Task succeeded: CheckM
[2023-03-18 08:17:42,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:17:42,748] [INFO] ===== Completeness check finished =====
[2023-03-18 08:17:42,748] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:17:42,749] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32483/markers.fasta)
[2023-03-18 08:17:42,749] [INFO] Task started: Blastn
[2023-03-18 08:17:42,749] [INFO] Running command: blastn -query OceanDNA-b32483/markers.fasta -db /var/lib/cwl/stg7df71b2f-9838-4268-8427-a1135ceeb0ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32483/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:43,660] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:43,661] [INFO] Selected 14 target genomes.
[2023-03-18 08:17:43,661] [INFO] Target genome list was writen to OceanDNA-b32483/target_genomes_gtdb.txt
[2023-03-18 08:17:43,683] [INFO] Task started: fastANI
[2023-03-18 08:17:43,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fb34425-83d6-4afd-8981-c40952ba1ba6/OceanDNA-b32483.fa --refList OceanDNA-b32483/target_genomes_gtdb.txt --output OceanDNA-b32483/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:17:46,428] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:46,430] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:17:46,431] [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_002689905.1	s__TMED131 sp002689905	99.9062	95	147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED131	95.0	100.00	100.00	0.83	0.83	2	conclusive
GCA_902615805.1	s__TMED62 sp902615805	76.7641	54	147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:17:46,431] [INFO] GTDB search result was written to OceanDNA-b32483/result_gtdb.tsv
[2023-03-18 08:17:46,431] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:17:46,431] [INFO] DFAST_QC result json was written to OceanDNA-b32483/dqc_result.json
[2023-03-18 08:17:46,432] [INFO] DFAST_QC completed!
[2023-03-18 08:17:46,432] [INFO] Total running time: 0h0m29s