[2023-03-15 11:22:20,467] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,467] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg89b2bae8-0fa2-470d-a408-76034536e166/dqc_reference
[2023-03-15 11:22:21,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,950] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,950] [INFO] Running command: cat /var/lib/cwl/stgb7f1224d-8b61-4fde-882a-825c5e681314/OceanDNA-b538.fa | prodigal -d OceanDNA-b538/cds.fna -a OceanDNA-b538/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:29,909] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:29,910] [INFO] Task started: HMMsearch
[2023-03-15 11:22:29,910] [INFO] Running command: hmmsearch --tblout OceanDNA-b538/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89b2bae8-0fa2-470d-a408-76034536e166/dqc_reference/reference_markers.hmm OceanDNA-b538/protein.faa > /dev/null
[2023-03-15 11:22:30,059] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:30,059] [INFO] Found 6/6 markers.
[2023-03-15 11:22:30,071] [INFO] Query marker FASTA was written to OceanDNA-b538/markers.fasta
[2023-03-15 11:22:30,072] [INFO] Task started: Blastn
[2023-03-15 11:22:30,072] [INFO] Running command: blastn -query OceanDNA-b538/markers.fasta -db /var/lib/cwl/stg89b2bae8-0fa2-470d-a408-76034536e166/dqc_reference/reference_markers.fasta -out OceanDNA-b538/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:30,585] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:30,586] [INFO] Selected 15 target genomes.
[2023-03-15 11:22:30,587] [INFO] Target genome list was writen to OceanDNA-b538/target_genomes.txt
[2023-03-15 11:22:30,596] [INFO] Task started: fastANI
[2023-03-15 11:22:30,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7f1224d-8b61-4fde-882a-825c5e681314/OceanDNA-b538.fa --refList OceanDNA-b538/target_genomes.txt --output OceanDNA-b538/fastani_result.tsv --threads 1
[2023-03-15 11:22:37,575] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:37,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89b2bae8-0fa2-470d-a408-76034536e166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:37,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89b2bae8-0fa2-470d-a408-76034536e166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:37,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:37,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:22:37,576] [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
--------------------------------------------------------------------------------
[2023-03-15 11:22:37,577] [INFO] DFAST Taxonomy check result was written to OceanDNA-b538/tc_result.tsv
[2023-03-15 11:22:37,577] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:37,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:37,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89b2bae8-0fa2-470d-a408-76034536e166/dqc_reference/checkm_data
[2023-03-15 11:22:37,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:37,583] [INFO] Task started: CheckM
[2023-03-15 11:22:37,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b538/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b538/checkm_input OceanDNA-b538/checkm_result
[2023-03-15 11:23:03,171] [INFO] Task succeeded: CheckM
[2023-03-15 11:23:03,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 3.07%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 11:23:03,173] [INFO] ===== Completeness check finished =====
[2023-03-15 11:23:03,174] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:23:03,174] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b538/markers.fasta)
[2023-03-15 11:23:03,174] [INFO] Task started: Blastn
[2023-03-15 11:23:03,174] [INFO] Running command: blastn -query OceanDNA-b538/markers.fasta -db /var/lib/cwl/stg89b2bae8-0fa2-470d-a408-76034536e166/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b538/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:23:04,022] [INFO] Task succeeded: Blastn
[2023-03-15 11:23:04,023] [INFO] Selected 15 target genomes.
[2023-03-15 11:23:04,023] [INFO] Target genome list was writen to OceanDNA-b538/target_genomes_gtdb.txt
[2023-03-15 11:23:04,034] [INFO] Task started: fastANI
[2023-03-15 11:23:04,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7f1224d-8b61-4fde-882a-825c5e681314/OceanDNA-b538.fa --refList OceanDNA-b538/target_genomes_gtdb.txt --output OceanDNA-b538/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:23:08,985] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:08,991] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:23:08,991] [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_001438985.1	s__UBA3006 sp001438985	98.9025	268	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	98.19	98.19	0.91	0.91	2	conclusive
GCA_014190095.1	s__UBA3006 sp014190095	81.7475	212	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903895515.1	s__UBA3006 sp903895515	80.9408	189	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	98.23	97.46	0.84	0.83	3	-
GCA_017853385.1	s__UBA3006 sp017853385	79.6605	181	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903850275.1	s__UBA3006 sp903850275	77.8881	76	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	96.61	96.61	0.70	0.70	2	-
GCA_002367695.1	s__UBA3006 sp002367695	77.6866	87	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	99.47	99.24	0.90	0.87	7	-
GCA_009701105.1	s__UBA3006 sp009701105	76.9875	55	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007279905.1	s__UBA3006 sp007279905	76.8905	58	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853285.1	s__UBA3006 sp903853285	76.8304	69	383	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	97.79	97.42	0.77	0.73	4	-
--------------------------------------------------------------------------------
[2023-03-15 11:23:08,991] [INFO] GTDB search result was written to OceanDNA-b538/result_gtdb.tsv
[2023-03-15 11:23:08,991] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:23:08,992] [INFO] DFAST_QC result json was written to OceanDNA-b538/dqc_result.json
[2023-03-15 11:23:08,992] [INFO] DFAST_QC completed!
[2023-03-15 11:23:08,992] [INFO] Total running time: 0h0m49s