[2023-03-15 11:51:17,347] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg862cb7c7-fa6a-442c-9451-67be71925fbb/dqc_reference
[2023-03-15 11:51:18,953] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,953] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,953] [INFO] Running command: cat /var/lib/cwl/stgf8ee0463-dea9-4541-b2be-b734a0d504c1/OceanDNA-b33609.fa | prodigal -d OceanDNA-b33609/cds.fna -a OceanDNA-b33609/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:32,281] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:32,281] [INFO] Task started: HMMsearch
[2023-03-15 11:51:32,281] [INFO] Running command: hmmsearch --tblout OceanDNA-b33609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg862cb7c7-fa6a-442c-9451-67be71925fbb/dqc_reference/reference_markers.hmm OceanDNA-b33609/protein.faa > /dev/null
[2023-03-15 11:51:32,454] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:32,455] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8ee0463-dea9-4541-b2be-b734a0d504c1/OceanDNA-b33609.fa]
[2023-03-15 11:51:32,472] [INFO] Query marker FASTA was written to OceanDNA-b33609/markers.fasta
[2023-03-15 11:51:32,473] [INFO] Task started: Blastn
[2023-03-15 11:51:32,473] [INFO] Running command: blastn -query OceanDNA-b33609/markers.fasta -db /var/lib/cwl/stg862cb7c7-fa6a-442c-9451-67be71925fbb/dqc_reference/reference_markers.fasta -out OceanDNA-b33609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:33,135] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:33,135] [INFO] Selected 19 target genomes.
[2023-03-15 11:51:33,136] [INFO] Target genome list was writen to OceanDNA-b33609/target_genomes.txt
[2023-03-15 11:51:33,148] [INFO] Task started: fastANI
[2023-03-15 11:51:33,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ee0463-dea9-4541-b2be-b734a0d504c1/OceanDNA-b33609.fa --refList OceanDNA-b33609/target_genomes.txt --output OceanDNA-b33609/fastani_result.tsv --threads 1
[2023-03-15 11:51:44,589] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:44,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg862cb7c7-fa6a-442c-9451-67be71925fbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:44,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg862cb7c7-fa6a-442c-9451-67be71925fbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:44,595] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:44,595] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:51:44,595] [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
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	79.9227	295	698	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	79.049	297	698	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	76.6413	52	698	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	76.3236	51	698	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	75.8365	53	698	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:51:44,595] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33609/tc_result.tsv
[2023-03-15 11:51:44,595] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:44,595] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:44,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg862cb7c7-fa6a-442c-9451-67be71925fbb/dqc_reference/checkm_data
[2023-03-15 11:51:44,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:44,600] [INFO] Task started: CheckM
[2023-03-15 11:51:44,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33609/checkm_input OceanDNA-b33609/checkm_result
[2023-03-15 11:52:21,672] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:21,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:21,675] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:21,675] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:21,675] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33609/markers.fasta)
[2023-03-15 11:52:21,676] [INFO] Task started: Blastn
[2023-03-15 11:52:21,676] [INFO] Running command: blastn -query OceanDNA-b33609/markers.fasta -db /var/lib/cwl/stg862cb7c7-fa6a-442c-9451-67be71925fbb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:22,746] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:22,747] [INFO] Selected 17 target genomes.
[2023-03-15 11:52:22,747] [INFO] Target genome list was writen to OceanDNA-b33609/target_genomes_gtdb.txt
[2023-03-15 11:52:22,766] [INFO] Task started: fastANI
[2023-03-15 11:52:22,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ee0463-dea9-4541-b2be-b734a0d504c1/OceanDNA-b33609.fa --refList OceanDNA-b33609/target_genomes_gtdb.txt --output OceanDNA-b33609/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:31,461] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:31,470] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:52:31,471] [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_010365175.1	s__Thiobacillus sp010365175	80.936	295	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256785.1	s__Thiobacillus sp002256785	80.7841	306	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780025.1	s__Thiobacillus sp018780025	80.2606	297	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820765.1	s__Thiobacillus sp018820765	79.6381	338	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.99	99.99	0.98	0.97	3	-
GCA_001899305.1	s__Thiobacillus sp001899305	79.446	322	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.65	95.89	0.93	0.87	5	-
GCF_001530125.1	s__Thiobacillus denitrificans_C	79.382	306	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897675.1	s__Thiobacillus sp001897675	79.2827	289	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	95.41	95.18	0.77	0.76	3	-
GCA_002343685.1	s__Thiobacillus denitrificans_A	79.2697	296	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.48	97.29	0.88	0.86	5	-
GCA_016124745.1	s__Thiobacillus sp016124745	79.212	283	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195805.1	s__Thiobacillus sp016195805	79.2111	282	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391285.1	s__Thiobacillus sp011391285	79.1733	276	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262815.1	s__Thiobacillus sp018262815	79.1573	238	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003510325.1	s__Thiobacillus sp003510325	79.0792	238	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.33	99.33	0.73	0.73	2	-
GCA_018780105.1	s__Thiobacillus sp018780105	79.0501	279	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373385.1	s__Thiobacillus thioparus	79.049	297	698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:31,471] [INFO] GTDB search result was written to OceanDNA-b33609/result_gtdb.tsv
[2023-03-15 11:52:31,471] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:31,472] [INFO] DFAST_QC result json was written to OceanDNA-b33609/dqc_result.json
[2023-03-15 11:52:31,472] [INFO] DFAST_QC completed!
[2023-03-15 11:52:31,472] [INFO] Total running time: 0h1m14s