[2023-03-18 22:16:20,345] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:16:20,345] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:16:20,345] [INFO] DQC Reference Directory: /var/lib/cwl/stgb250460c-4c3d-4d3b-91bc-4ccf10965041/dqc_reference
[2023-03-18 22:16:21,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:16:21,451] [INFO] Task started: Prodigal
[2023-03-18 22:16:21,451] [INFO] Running command: cat /var/lib/cwl/stg75e298e3-0e35-4ee5-a8fa-43a6870c5753/OceanDNA-b24493.fa | prodigal -d OceanDNA-b24493/cds.fna -a OceanDNA-b24493/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:16:25,859] [INFO] Task succeeded: Prodigal
[2023-03-18 22:16:25,860] [INFO] Task started: HMMsearch
[2023-03-18 22:16:25,860] [INFO] Running command: hmmsearch --tblout OceanDNA-b24493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb250460c-4c3d-4d3b-91bc-4ccf10965041/dqc_reference/reference_markers.hmm OceanDNA-b24493/protein.faa > /dev/null
[2023-03-18 22:16:26,005] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:16:26,006] [INFO] Found 6/6 markers.
[2023-03-18 22:16:26,015] [INFO] Query marker FASTA was written to OceanDNA-b24493/markers.fasta
[2023-03-18 22:16:26,016] [INFO] Task started: Blastn
[2023-03-18 22:16:26,016] [INFO] Running command: blastn -query OceanDNA-b24493/markers.fasta -db /var/lib/cwl/stgb250460c-4c3d-4d3b-91bc-4ccf10965041/dqc_reference/reference_markers.fasta -out OceanDNA-b24493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:16:26,572] [INFO] Task succeeded: Blastn
[2023-03-18 22:16:26,573] [INFO] Selected 13 target genomes.
[2023-03-18 22:16:26,573] [INFO] Target genome list was writen to OceanDNA-b24493/target_genomes.txt
[2023-03-18 22:16:26,583] [INFO] Task started: fastANI
[2023-03-18 22:16:26,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg75e298e3-0e35-4ee5-a8fa-43a6870c5753/OceanDNA-b24493.fa --refList OceanDNA-b24493/target_genomes.txt --output OceanDNA-b24493/fastani_result.tsv --threads 1
[2023-03-18 22:16:32,805] [INFO] Task succeeded: fastANI
[2023-03-18 22:16:32,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb250460c-4c3d-4d3b-91bc-4ccf10965041/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:16:32,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb250460c-4c3d-4d3b-91bc-4ccf10965041/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:16:32,806] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:16:32,806] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:16:32,806] [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 22:16:32,807] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24493/tc_result.tsv
[2023-03-18 22:16:32,807] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:16:32,807] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:16:32,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb250460c-4c3d-4d3b-91bc-4ccf10965041/dqc_reference/checkm_data
[2023-03-18 22:16:32,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:16:32,813] [INFO] Task started: CheckM
[2023-03-18 22:16:32,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24493/checkm_input OceanDNA-b24493/checkm_result
[2023-03-18 22:16:50,468] [INFO] Task succeeded: CheckM
[2023-03-18 22:16:50,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.59%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:16:50,471] [INFO] ===== Completeness check finished =====
[2023-03-18 22:16:50,471] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:16:50,471] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24493/markers.fasta)
[2023-03-18 22:16:50,472] [INFO] Task started: Blastn
[2023-03-18 22:16:50,472] [INFO] Running command: blastn -query OceanDNA-b24493/markers.fasta -db /var/lib/cwl/stgb250460c-4c3d-4d3b-91bc-4ccf10965041/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:16:51,346] [INFO] Task succeeded: Blastn
[2023-03-18 22:16:51,347] [INFO] Selected 16 target genomes.
[2023-03-18 22:16:51,347] [INFO] Target genome list was writen to OceanDNA-b24493/target_genomes_gtdb.txt
[2023-03-18 22:16:51,366] [INFO] Task started: fastANI
[2023-03-18 22:16:51,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg75e298e3-0e35-4ee5-a8fa-43a6870c5753/OceanDNA-b24493.fa --refList OceanDNA-b24493/target_genomes_gtdb.txt --output OceanDNA-b24493/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:16:54,172] [INFO] Task succeeded: fastANI
[2023-03-18 22:16:54,180] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:16:54,186] [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_008638215.1	s__HIMB59 sp008638215	97.9764	173	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.46	99.38	0.89	0.85	4	conclusive
GCA_000299115.1	s__HIMB59 sp000299115	83.2493	151	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529795.1	s__HIMB59 sp902529795	81.8598	97	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522585.1	s__HIMB59 sp902522585	81.7358	96	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574995.1	s__HIMB59 sp902574995	77.8168	52	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004321805.1	s__HIMB59 sp004321805	77.7966	75	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601865.1	s__HIMB59 sp902601865	77.5277	61	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524245.1	s__HIMB59 sp902524245	77.3828	58	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.23	0.87	0.86	3	-
GCA_902621205.1	s__HIMB59 sp902621205	77.292	61	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.28	98.69	0.88	0.86	4	-
GCA_902521795.1	s__HIMB59 sp902560595	77.0852	56	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.49	95.27	0.76	0.73	4	-
GCA_902530745.1	s__HIMB59 sp902530745	77.0317	57	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.01	95.70	0.83	0.77	8	-
GCA_902599045.1	s__HIMB59 sp902615815	76.8391	64	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.41	95.18	0.86	0.81	23	-
GCA_902521485.1	s__HIMB59 sp902521485	76.7102	53	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	98.22	98.22	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:16:54,186] [INFO] GTDB search result was written to OceanDNA-b24493/result_gtdb.tsv
[2023-03-18 22:16:54,187] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:16:54,188] [INFO] DFAST_QC result json was written to OceanDNA-b24493/dqc_result.json
[2023-03-18 22:16:54,188] [INFO] DFAST_QC completed!
[2023-03-18 22:16:54,188] [INFO] Total running time: 0h0m34s