[2023-03-17 22:37:12,601] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:12,601] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:12,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgd53f60b6-ea02-4519-92e3-7bfc58527baa/dqc_reference
[2023-03-17 22:37:14,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:14,350] [INFO] Task started: Prodigal
[2023-03-17 22:37:14,350] [INFO] Running command: cat /var/lib/cwl/stga5945169-d243-4ba1-ac16-b866537e9a35/OceanDNA-b25995.fa | prodigal -d OceanDNA-b25995/cds.fna -a OceanDNA-b25995/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:20,022] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:20,022] [INFO] Task started: HMMsearch
[2023-03-17 22:37:20,022] [INFO] Running command: hmmsearch --tblout OceanDNA-b25995/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd53f60b6-ea02-4519-92e3-7bfc58527baa/dqc_reference/reference_markers.hmm OceanDNA-b25995/protein.faa > /dev/null
[2023-03-17 22:37:20,171] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:20,172] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga5945169-d243-4ba1-ac16-b866537e9a35/OceanDNA-b25995.fa]
[2023-03-17 22:37:20,182] [INFO] Query marker FASTA was written to OceanDNA-b25995/markers.fasta
[2023-03-17 22:37:20,182] [INFO] Task started: Blastn
[2023-03-17 22:37:20,182] [INFO] Running command: blastn -query OceanDNA-b25995/markers.fasta -db /var/lib/cwl/stgd53f60b6-ea02-4519-92e3-7bfc58527baa/dqc_reference/reference_markers.fasta -out OceanDNA-b25995/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:21,458] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:21,459] [INFO] Selected 20 target genomes.
[2023-03-17 22:37:21,459] [INFO] Target genome list was writen to OceanDNA-b25995/target_genomes.txt
[2023-03-17 22:37:21,471] [INFO] Task started: fastANI
[2023-03-17 22:37:21,471] [INFO] Running command: fastANI --query /var/lib/cwl/stga5945169-d243-4ba1-ac16-b866537e9a35/OceanDNA-b25995.fa --refList OceanDNA-b25995/target_genomes.txt --output OceanDNA-b25995/fastani_result.tsv --threads 1
[2023-03-17 22:37:28,267] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:28,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd53f60b6-ea02-4519-92e3-7bfc58527baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:37:28,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd53f60b6-ea02-4519-92e3-7bfc58527baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:37:28,268] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:37:28,268] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:37:28,268] [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
--------------------------------------------------------------------------------
[2023-03-17 22:37:28,268] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25995/tc_result.tsv
[2023-03-17 22:37:28,268] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:37:28,268] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:37:28,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd53f60b6-ea02-4519-92e3-7bfc58527baa/dqc_reference/checkm_data
[2023-03-17 22:37:28,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:37:28,284] [INFO] Task started: CheckM
[2023-03-17 22:37:28,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25995/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25995/checkm_input OceanDNA-b25995/checkm_result
[2023-03-17 22:37:48,994] [INFO] Task succeeded: CheckM
[2023-03-17 22:37:48,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 22:37:48,996] [INFO] ===== Completeness check finished =====
[2023-03-17 22:37:48,997] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:37:48,997] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25995/markers.fasta)
[2023-03-17 22:37:48,997] [INFO] Task started: Blastn
[2023-03-17 22:37:48,997] [INFO] Running command: blastn -query OceanDNA-b25995/markers.fasta -db /var/lib/cwl/stgd53f60b6-ea02-4519-92e3-7bfc58527baa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25995/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:49,648] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:49,648] [INFO] Selected 16 target genomes.
[2023-03-17 22:37:49,649] [INFO] Target genome list was writen to OceanDNA-b25995/target_genomes_gtdb.txt
[2023-03-17 22:37:49,747] [INFO] Task started: fastANI
[2023-03-17 22:37:49,747] [INFO] Running command: fastANI --query /var/lib/cwl/stga5945169-d243-4ba1-ac16-b866537e9a35/OceanDNA-b25995.fa --refList OceanDNA-b25995/target_genomes_gtdb.txt --output OceanDNA-b25995/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:37:54,791] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:54,801] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:37:54,801] [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_902619805.1	s__AAA536-G10 sp902619805	90.1655	312	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558885.1	s__AAA536-G10 sp902558885	89.6567	278	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589185.1	s__AAA536-G10 sp902589185	89.4283	231	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543145.1	s__AAA536-G10 sp902543145	89.2	285	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	99.74	99.74	0.81	0.81	2	-
GCA_902517815.1	s__AAA536-G10 sp902517815	89.0615	311	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529515.1	s__AAA536-G10 sp902529515	89.024	210	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.18	97.18	0.52	0.52	2	-
GCA_902619485.1	s__AAA536-G10 sp902619485	88.7623	261	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902539895.1	s__AAA536-G10 sp902539895	88.7046	192	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542765.1	s__AAA536-G10 sp902542765	88.6528	163	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595145.1	s__AAA536-G10 sp902595145	88.5447	228	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583415.1	s__AAA536-G10 sp902583415	88.483	230	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623995.1	s__AAA536-G10 sp902623995	88.4277	324	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.83	98.83	0.84	0.84	2	-
GCA_902592615.1	s__AAA536-G10 sp902592615	87.3038	235	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537945.1	s__AAA536-G10 sp902537945	87.0684	292	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593735.1	s__AAA536-G10 sp902593735	85.8006	243	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284565.1	s__AAA536-G10 sp003284565	85.5227	267	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:37:54,801] [INFO] GTDB search result was written to OceanDNA-b25995/result_gtdb.tsv
[2023-03-17 22:37:54,801] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:37:54,802] [INFO] DFAST_QC result json was written to OceanDNA-b25995/dqc_result.json
[2023-03-17 22:37:54,802] [INFO] DFAST_QC completed!
[2023-03-17 22:37:54,802] [INFO] Total running time: 0h0m42s