[2023-03-18 10:53:04,369] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:53:04,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:53:04,371] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0a7bd4b-e02a-4b11-a374-83e973ce087a/dqc_reference
[2023-03-18 10:53:05,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:53:05,472] [INFO] Task started: Prodigal
[2023-03-18 10:53:05,472] [INFO] Running command: cat /var/lib/cwl/stg1c55887c-819e-4d8c-a6c5-597cef5409bf/OceanDNA-b46168.fa | prodigal -d OceanDNA-b46168/cds.fna -a OceanDNA-b46168/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:53:18,550] [INFO] Task succeeded: Prodigal
[2023-03-18 10:53:18,550] [INFO] Task started: HMMsearch
[2023-03-18 10:53:18,550] [INFO] Running command: hmmsearch --tblout OceanDNA-b46168/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0a7bd4b-e02a-4b11-a374-83e973ce087a/dqc_reference/reference_markers.hmm OceanDNA-b46168/protein.faa > /dev/null
[2023-03-18 10:53:18,707] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:53:18,708] [INFO] Found 6/6 markers.
[2023-03-18 10:53:18,722] [INFO] Query marker FASTA was written to OceanDNA-b46168/markers.fasta
[2023-03-18 10:53:18,724] [INFO] Task started: Blastn
[2023-03-18 10:53:18,724] [INFO] Running command: blastn -query OceanDNA-b46168/markers.fasta -db /var/lib/cwl/stgd0a7bd4b-e02a-4b11-a374-83e973ce087a/dqc_reference/reference_markers.fasta -out OceanDNA-b46168/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:53:19,440] [INFO] Task succeeded: Blastn
[2023-03-18 10:53:19,447] [INFO] Selected 20 target genomes.
[2023-03-18 10:53:19,448] [INFO] Target genome list was writen to OceanDNA-b46168/target_genomes.txt
[2023-03-18 10:53:19,461] [INFO] Task started: fastANI
[2023-03-18 10:53:19,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c55887c-819e-4d8c-a6c5-597cef5409bf/OceanDNA-b46168.fa --refList OceanDNA-b46168/target_genomes.txt --output OceanDNA-b46168/fastani_result.tsv --threads 1
[2023-03-18 10:53:32,380] [INFO] Task succeeded: fastANI
[2023-03-18 10:53:32,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0a7bd4b-e02a-4b11-a374-83e973ce087a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:53:32,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0a7bd4b-e02a-4b11-a374-83e973ce087a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:53:32,384] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:53:32,384] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:53:32,384] [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
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.7744	65	493	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:53:32,385] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46168/tc_result.tsv
[2023-03-18 10:53:32,386] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:53:32,386] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:53:32,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0a7bd4b-e02a-4b11-a374-83e973ce087a/dqc_reference/checkm_data
[2023-03-18 10:53:32,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:53:32,402] [INFO] Task started: CheckM
[2023-03-18 10:53:32,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46168/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46168/checkm_input OceanDNA-b46168/checkm_result
[2023-03-18 10:54:08,908] [INFO] Task succeeded: CheckM
[2023-03-18 10:54:08,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:54:08,915] [INFO] ===== Completeness check finished =====
[2023-03-18 10:54:08,915] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:54:08,915] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46168/markers.fasta)
[2023-03-18 10:54:08,917] [INFO] Task started: Blastn
[2023-03-18 10:54:08,917] [INFO] Running command: blastn -query OceanDNA-b46168/markers.fasta -db /var/lib/cwl/stgd0a7bd4b-e02a-4b11-a374-83e973ce087a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46168/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:54:09,884] [INFO] Task succeeded: Blastn
[2023-03-18 10:54:09,887] [INFO] Selected 23 target genomes.
[2023-03-18 10:54:09,887] [INFO] Target genome list was writen to OceanDNA-b46168/target_genomes_gtdb.txt
[2023-03-18 10:54:09,902] [INFO] Task started: fastANI
[2023-03-18 10:54:09,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c55887c-819e-4d8c-a6c5-597cef5409bf/OceanDNA-b46168.fa --refList OceanDNA-b46168/target_genomes_gtdb.txt --output OceanDNA-b46168/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:54:21,152] [INFO] Task succeeded: fastANI
[2023-03-18 10:54:21,156] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:54:21,156] [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
GCF_003185655.1	s__WN38 sp003185655	76.7744	65	493	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728235.1	s__BACL24 sp902728235	76.5867	56	493	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.30	98.39	0.95	0.90	8	-
GCA_002729725.1	s__UBA7441 sp002729725	76.4298	61	493	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	-
GCA_002480015.1	s__UBA7441 sp002480015	76.174	50	493	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.46	97.23	0.80	0.69	7	-
GCA_002430605.1	s__BACL24 sp002430605	75.8814	61	493	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.69	99.69	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-18 10:54:21,159] [INFO] GTDB search result was written to OceanDNA-b46168/result_gtdb.tsv
[2023-03-18 10:54:21,161] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:54:21,166] [INFO] DFAST_QC result json was written to OceanDNA-b46168/dqc_result.json
[2023-03-18 10:54:21,166] [INFO] DFAST_QC completed!
[2023-03-18 10:54:21,166] [INFO] Total running time: 0h1m17s