[2023-03-19 00:01:03,276] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,276] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,276] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3de4cea-97a5-4801-b059-cbb8c359993a/dqc_reference
[2023-03-19 00:01:04,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,447] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,448] [INFO] Running command: cat /var/lib/cwl/stg4add8cc0-a68f-43bb-a50f-150ac65cf1e4/OceanDNA-b46722.fa | prodigal -d OceanDNA-b46722/cds.fna -a OceanDNA-b46722/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:30,350] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:30,350] [INFO] Task started: HMMsearch
[2023-03-19 00:01:30,350] [INFO] Running command: hmmsearch --tblout OceanDNA-b46722/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3de4cea-97a5-4801-b059-cbb8c359993a/dqc_reference/reference_markers.hmm OceanDNA-b46722/protein.faa > /dev/null
[2023-03-19 00:01:30,664] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:30,664] [INFO] Found 6/6 markers.
[2023-03-19 00:01:30,686] [INFO] Query marker FASTA was written to OceanDNA-b46722/markers.fasta
[2023-03-19 00:01:30,686] [INFO] Task started: Blastn
[2023-03-19 00:01:30,687] [INFO] Running command: blastn -query OceanDNA-b46722/markers.fasta -db /var/lib/cwl/stgd3de4cea-97a5-4801-b059-cbb8c359993a/dqc_reference/reference_markers.fasta -out OceanDNA-b46722/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:31,214] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:31,224] [INFO] Selected 19 target genomes.
[2023-03-19 00:01:31,225] [INFO] Target genome list was writen to OceanDNA-b46722/target_genomes.txt
[2023-03-19 00:01:31,236] [INFO] Task started: fastANI
[2023-03-19 00:01:31,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg4add8cc0-a68f-43bb-a50f-150ac65cf1e4/OceanDNA-b46722.fa --refList OceanDNA-b46722/target_genomes.txt --output OceanDNA-b46722/fastani_result.tsv --threads 1
[2023-03-19 00:01:44,736] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:44,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3de4cea-97a5-4801-b059-cbb8c359993a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:44,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3de4cea-97a5-4801-b059-cbb8c359993a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:44,737] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:44,737] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:44,737] [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
--------------------------------------------------------------------------------
[2023-03-19 00:01:44,737] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46722/tc_result.tsv
[2023-03-19 00:01:44,737] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:44,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:44,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3de4cea-97a5-4801-b059-cbb8c359993a/dqc_reference/checkm_data
[2023-03-19 00:01:44,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:44,775] [INFO] Task started: CheckM
[2023-03-19 00:01:44,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46722/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46722/checkm_input OceanDNA-b46722/checkm_result
[2023-03-19 00:02:50,149] [INFO] Task succeeded: CheckM
[2023-03-19 00:02:50,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:02:50,152] [INFO] ===== Completeness check finished =====
[2023-03-19 00:02:50,152] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:02:50,152] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46722/markers.fasta)
[2023-03-19 00:02:50,152] [INFO] Task started: Blastn
[2023-03-19 00:02:50,152] [INFO] Running command: blastn -query OceanDNA-b46722/markers.fasta -db /var/lib/cwl/stgd3de4cea-97a5-4801-b059-cbb8c359993a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46722/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:02:50,866] [INFO] Task succeeded: Blastn
[2023-03-19 00:02:50,866] [INFO] Selected 7 target genomes.
[2023-03-19 00:02:50,866] [INFO] Target genome list was writen to OceanDNA-b46722/target_genomes_gtdb.txt
[2023-03-19 00:02:50,937] [INFO] Task started: fastANI
[2023-03-19 00:02:50,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg4add8cc0-a68f-43bb-a50f-150ac65cf1e4/OceanDNA-b46722.fa --refList OceanDNA-b46722/target_genomes_gtdb.txt --output OceanDNA-b46722/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:56,456] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:56,461] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:02:56,461] [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_002686085.1	s__Roseibacillus_B sp002686085	99.1697	1004	1038	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.30	99.30	0.96	0.96	3	conclusive
GCA_002380675.1	s__Roseibacillus_B sp002380675	93.8552	793	1038	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	99.08	0.81	0.81	2	-
GCA_002420305.1	s__Roseibacillus_B sp002420305	93.4944	892	1038	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.44	96.53	0.87	0.86	5	-
GCA_002709915.1	s__Roseibacillus_B sp002709915	85.2442	818	1038	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.45	99.45	0.86	0.86	2	-
GCA_002715825.1	s__Roseibacillus_B sp002715825	84.0406	826	1038	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	98.76	0.87	0.85	4	-
GCA_002729275.1	s__Roseibacillus_B sp002729275	82.9745	769	1038	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	98.94	98.88	0.91	0.89	3	-
GCA_002723015.1	s__Roseibacillus_B sp002723015	79.0851	521	1038	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.32	99.32	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:56,461] [INFO] GTDB search result was written to OceanDNA-b46722/result_gtdb.tsv
[2023-03-19 00:02:56,461] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:56,462] [INFO] DFAST_QC result json was written to OceanDNA-b46722/dqc_result.json
[2023-03-19 00:02:56,462] [INFO] DFAST_QC completed!
[2023-03-19 00:02:56,462] [INFO] Total running time: 0h1m53s