[2023-03-18 07:54:30,541] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:30,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:30,541] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcba3962-7f60-4396-909e-3343cd4e63b7/dqc_reference
[2023-03-18 07:54:32,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:32,272] [INFO] Task started: Prodigal
[2023-03-18 07:54:32,272] [INFO] Running command: cat /var/lib/cwl/stg29150b28-932a-427f-b76a-f8d8b297b018/OceanDNA-b26585.fa | prodigal -d OceanDNA-b26585/cds.fna -a OceanDNA-b26585/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:41,889] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:41,889] [INFO] Task started: HMMsearch
[2023-03-18 07:54:41,889] [INFO] Running command: hmmsearch --tblout OceanDNA-b26585/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcba3962-7f60-4396-909e-3343cd4e63b7/dqc_reference/reference_markers.hmm OceanDNA-b26585/protein.faa > /dev/null
[2023-03-18 07:54:42,050] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:42,051] [INFO] Found 6/6 markers.
[2023-03-18 07:54:42,064] [INFO] Query marker FASTA was written to OceanDNA-b26585/markers.fasta
[2023-03-18 07:54:42,065] [INFO] Task started: Blastn
[2023-03-18 07:54:42,065] [INFO] Running command: blastn -query OceanDNA-b26585/markers.fasta -db /var/lib/cwl/stgbcba3962-7f60-4396-909e-3343cd4e63b7/dqc_reference/reference_markers.fasta -out OceanDNA-b26585/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:42,639] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:42,640] [INFO] Selected 30 target genomes.
[2023-03-18 07:54:42,640] [INFO] Target genome list was writen to OceanDNA-b26585/target_genomes.txt
[2023-03-18 07:54:42,659] [INFO] Task started: fastANI
[2023-03-18 07:54:42,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg29150b28-932a-427f-b76a-f8d8b297b018/OceanDNA-b26585.fa --refList OceanDNA-b26585/target_genomes.txt --output OceanDNA-b26585/fastani_result.tsv --threads 1
[2023-03-18 07:55:04,875] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:04,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcba3962-7f60-4396-909e-3343cd4e63b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:55:04,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcba3962-7f60-4396-909e-3343cd4e63b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:55:04,876] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:55:04,876] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:55:04,876] [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 07:55:04,876] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26585/tc_result.tsv
[2023-03-18 07:55:04,876] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:55:04,877] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:55:04,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcba3962-7f60-4396-909e-3343cd4e63b7/dqc_reference/checkm_data
[2023-03-18 07:55:04,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:55:04,885] [INFO] Task started: CheckM
[2023-03-18 07:55:04,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26585/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26585/checkm_input OceanDNA-b26585/checkm_result
[2023-03-18 07:55:34,482] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:34,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.29%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:34,485] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:34,485] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:34,485] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26585/markers.fasta)
[2023-03-18 07:55:34,486] [INFO] Task started: Blastn
[2023-03-18 07:55:34,486] [INFO] Running command: blastn -query OceanDNA-b26585/markers.fasta -db /var/lib/cwl/stgbcba3962-7f60-4396-909e-3343cd4e63b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26585/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:35,387] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:35,388] [INFO] Selected 28 target genomes.
[2023-03-18 07:55:35,388] [INFO] Target genome list was writen to OceanDNA-b26585/target_genomes_gtdb.txt
[2023-03-18 07:55:35,477] [INFO] Task started: fastANI
[2023-03-18 07:55:35,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg29150b28-932a-427f-b76a-f8d8b297b018/OceanDNA-b26585.fa --refList OceanDNA-b26585/target_genomes_gtdb.txt --output OceanDNA-b26585/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:55:48,613] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:48,615] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:55:48,615] [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_002457135.1	s__UBA1172 sp002457135	77.5048	138	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA1172	95.0	99.36	98.87	0.81	0.72	9	-
GCA_011522975.1	s__UBA1172 sp011522975	76.355	72	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA1172	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:55:48,616] [INFO] GTDB search result was written to OceanDNA-b26585/result_gtdb.tsv
[2023-03-18 07:55:48,616] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:55:48,616] [INFO] DFAST_QC result json was written to OceanDNA-b26585/dqc_result.json
[2023-03-18 07:55:48,616] [INFO] DFAST_QC completed!
[2023-03-18 07:55:48,616] [INFO] Total running time: 0h1m18s