[2023-03-15 08:21:23,621] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:21:23,622] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:21:23,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg33e85e57-2a12-499f-a923-7cc6bb7ab338/dqc_reference
[2023-03-15 08:21:24,707] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:21:24,707] [INFO] Task started: Prodigal
[2023-03-15 08:21:24,707] [INFO] Running command: cat /var/lib/cwl/stg9e583a7b-949d-4e1d-97be-9101ca88bab2/OceanDNA-b5067.fa | prodigal -d OceanDNA-b5067/cds.fna -a OceanDNA-b5067/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:21:30,268] [INFO] Task succeeded: Prodigal
[2023-03-15 08:21:30,269] [INFO] Task started: HMMsearch
[2023-03-15 08:21:30,269] [INFO] Running command: hmmsearch --tblout OceanDNA-b5067/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33e85e57-2a12-499f-a923-7cc6bb7ab338/dqc_reference/reference_markers.hmm OceanDNA-b5067/protein.faa > /dev/null
[2023-03-15 08:21:30,402] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:21:30,403] [INFO] Found 6/6 markers.
[2023-03-15 08:21:30,415] [INFO] Query marker FASTA was written to OceanDNA-b5067/markers.fasta
[2023-03-15 08:21:30,417] [INFO] Task started: Blastn
[2023-03-15 08:21:30,417] [INFO] Running command: blastn -query OceanDNA-b5067/markers.fasta -db /var/lib/cwl/stg33e85e57-2a12-499f-a923-7cc6bb7ab338/dqc_reference/reference_markers.fasta -out OceanDNA-b5067/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:21:30,979] [INFO] Task succeeded: Blastn
[2023-03-15 08:21:30,981] [INFO] Selected 24 target genomes.
[2023-03-15 08:21:30,981] [INFO] Target genome list was writen to OceanDNA-b5067/target_genomes.txt
[2023-03-15 08:21:30,997] [INFO] Task started: fastANI
[2023-03-15 08:21:30,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e583a7b-949d-4e1d-97be-9101ca88bab2/OceanDNA-b5067.fa --refList OceanDNA-b5067/target_genomes.txt --output OceanDNA-b5067/fastani_result.tsv --threads 1
[2023-03-15 08:21:43,430] [INFO] Task succeeded: fastANI
[2023-03-15 08:21:43,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33e85e57-2a12-499f-a923-7cc6bb7ab338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:21:43,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33e85e57-2a12-499f-a923-7cc6bb7ab338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:21:43,431] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:21:43,431] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:21:43,431] [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 08:21:43,432] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5067/tc_result.tsv
[2023-03-15 08:21:43,433] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:21:43,433] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:21:43,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33e85e57-2a12-499f-a923-7cc6bb7ab338/dqc_reference/checkm_data
[2023-03-15 08:21:43,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:21:43,448] [INFO] Task started: CheckM
[2023-03-15 08:21:43,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5067/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5067/checkm_input OceanDNA-b5067/checkm_result
[2023-03-15 08:22:03,042] [INFO] Task succeeded: CheckM
[2023-03-15 08:22:03,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:22:03,074] [INFO] ===== Completeness check finished =====
[2023-03-15 08:22:03,074] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:22:03,074] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5067/markers.fasta)
[2023-03-15 08:22:03,076] [INFO] Task started: Blastn
[2023-03-15 08:22:03,076] [INFO] Running command: blastn -query OceanDNA-b5067/markers.fasta -db /var/lib/cwl/stg33e85e57-2a12-499f-a923-7cc6bb7ab338/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5067/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:22:03,806] [INFO] Task succeeded: Blastn
[2023-03-15 08:22:03,809] [INFO] Selected 10 target genomes.
[2023-03-15 08:22:03,809] [INFO] Target genome list was writen to OceanDNA-b5067/target_genomes_gtdb.txt
[2023-03-15 08:22:03,822] [INFO] Task started: fastANI
[2023-03-15 08:22:03,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e583a7b-949d-4e1d-97be-9101ca88bab2/OceanDNA-b5067.fa --refList OceanDNA-b5067/target_genomes_gtdb.txt --output OceanDNA-b5067/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:22:06,186] [INFO] Task succeeded: fastANI
[2023-03-15 08:22:06,192] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:22:06,192] [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_018645865.1	s__UWMA-0277 sp018645865	99.6624	198	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	conclusive
GCA_014384505.1	s__UWMA-0277 sp014384505	88.0031	172	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181635.1	s__UWMA-0277 sp905181635	85.0887	133	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182255.1	s__UWMA-0277 sp905182255	84.6322	106	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664745.1	s__UWMA-0277 sp018664745	81.4441	150	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612305.1	s__UWMA-0277 sp905612305	80.1893	123	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960805.1	s__UWMA-0277 sp012960805	80.0792	145	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	79.8046	136	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_905479165.1	s__UWMA-0277 sp905479165	79.5719	123	238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:22:06,193] [INFO] GTDB search result was written to OceanDNA-b5067/result_gtdb.tsv
[2023-03-15 08:22:06,194] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:22:06,195] [INFO] DFAST_QC result json was written to OceanDNA-b5067/dqc_result.json
[2023-03-15 08:22:06,195] [INFO] DFAST_QC completed!
[2023-03-15 08:22:06,195] [INFO] Total running time: 0h0m43s