[2023-03-17 10:35:02,805] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:35:02,805] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:35:02,805] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8d5643e-8c03-4940-8e05-e22b24e308a6/dqc_reference
[2023-03-17 10:35:04,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:35:04,550] [INFO] Task started: Prodigal
[2023-03-17 10:35:04,550] [INFO] Running command: cat /var/lib/cwl/stga58add72-da46-44e7-a831-5f2765f38d9f/OceanDNA-b30743.fa | prodigal -d OceanDNA-b30743/cds.fna -a OceanDNA-b30743/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:35:24,448] [INFO] Task succeeded: Prodigal
[2023-03-17 10:35:24,448] [INFO] Task started: HMMsearch
[2023-03-17 10:35:24,448] [INFO] Running command: hmmsearch --tblout OceanDNA-b30743/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8d5643e-8c03-4940-8e05-e22b24e308a6/dqc_reference/reference_markers.hmm OceanDNA-b30743/protein.faa > /dev/null
[2023-03-17 10:35:24,662] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:35:24,663] [INFO] Found 6/6 markers.
[2023-03-17 10:35:24,688] [INFO] Query marker FASTA was written to OceanDNA-b30743/markers.fasta
[2023-03-17 10:35:24,690] [INFO] Task started: Blastn
[2023-03-17 10:35:24,690] [INFO] Running command: blastn -query OceanDNA-b30743/markers.fasta -db /var/lib/cwl/stgf8d5643e-8c03-4940-8e05-e22b24e308a6/dqc_reference/reference_markers.fasta -out OceanDNA-b30743/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:25,300] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:25,301] [INFO] Selected 27 target genomes.
[2023-03-17 10:35:25,301] [INFO] Target genome list was writen to OceanDNA-b30743/target_genomes.txt
[2023-03-17 10:35:25,317] [INFO] Task started: fastANI
[2023-03-17 10:35:25,317] [INFO] Running command: fastANI --query /var/lib/cwl/stga58add72-da46-44e7-a831-5f2765f38d9f/OceanDNA-b30743.fa --refList OceanDNA-b30743/target_genomes.txt --output OceanDNA-b30743/fastani_result.tsv --threads 1
[2023-03-17 10:35:43,684] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:43,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8d5643e-8c03-4940-8e05-e22b24e308a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:35:43,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8d5643e-8c03-4940-8e05-e22b24e308a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:35:43,685] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:35:43,685] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:35:43,685] [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
--------------------------------------------------------------------------------
[2023-03-17 10:35:43,685] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30743/tc_result.tsv
[2023-03-17 10:35:43,685] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:35:43,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:35:43,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8d5643e-8c03-4940-8e05-e22b24e308a6/dqc_reference/checkm_data
[2023-03-17 10:35:43,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:35:43,700] [INFO] Task started: CheckM
[2023-03-17 10:35:43,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30743/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30743/checkm_input OceanDNA-b30743/checkm_result
[2023-03-17 10:36:34,928] [INFO] Task succeeded: CheckM
[2023-03-17 10:36:34,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 1.36%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:36:34,931] [INFO] ===== Completeness check finished =====
[2023-03-17 10:36:34,932] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:36:34,932] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30743/markers.fasta)
[2023-03-17 10:36:34,933] [INFO] Task started: Blastn
[2023-03-17 10:36:34,933] [INFO] Running command: blastn -query OceanDNA-b30743/markers.fasta -db /var/lib/cwl/stgf8d5643e-8c03-4940-8e05-e22b24e308a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30743/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:36:35,987] [INFO] Task succeeded: Blastn
[2023-03-17 10:36:35,988] [INFO] Selected 31 target genomes.
[2023-03-17 10:36:35,988] [INFO] Target genome list was writen to OceanDNA-b30743/target_genomes_gtdb.txt
[2023-03-17 10:36:36,900] [INFO] Task started: fastANI
[2023-03-17 10:36:36,900] [INFO] Running command: fastANI --query /var/lib/cwl/stga58add72-da46-44e7-a831-5f2765f38d9f/OceanDNA-b30743.fa --refList OceanDNA-b30743/target_genomes_gtdb.txt --output OceanDNA-b30743/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:36:53,228] [INFO] Task succeeded: fastANI
[2023-03-17 10:36:53,230] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:36:53,230] [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_018660465.1	s__JABJKH01 sp018660465	99.8871	1020	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JABJKH01;g__JABJKH01	95.0	99.88	99.82	0.92	0.90	5	conclusive
--------------------------------------------------------------------------------
[2023-03-17 10:36:53,230] [INFO] GTDB search result was written to OceanDNA-b30743/result_gtdb.tsv
[2023-03-17 10:36:53,231] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:36:53,231] [INFO] DFAST_QC result json was written to OceanDNA-b30743/dqc_result.json
[2023-03-17 10:36:53,231] [INFO] DFAST_QC completed!
[2023-03-17 10:36:53,231] [INFO] Total running time: 0h1m50s