[2023-03-16 20:47:10,581] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:47:10,582] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:47:10,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg1707ed33-c30a-4a8a-87dc-bcef53c9334d/dqc_reference
[2023-03-16 20:47:11,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:47:11,664] [INFO] Task started: Prodigal
[2023-03-16 20:47:11,664] [INFO] Running command: cat /var/lib/cwl/stgbfb33933-3a92-4a1a-afe5-3fd953e4f8f5/OceanDNA-b13475.fa | prodigal -d OceanDNA-b13475/cds.fna -a OceanDNA-b13475/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:47:18,616] [INFO] Task succeeded: Prodigal
[2023-03-16 20:47:18,616] [INFO] Task started: HMMsearch
[2023-03-16 20:47:18,616] [INFO] Running command: hmmsearch --tblout OceanDNA-b13475/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1707ed33-c30a-4a8a-87dc-bcef53c9334d/dqc_reference/reference_markers.hmm OceanDNA-b13475/protein.faa > /dev/null
[2023-03-16 20:47:18,770] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:47:18,771] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbfb33933-3a92-4a1a-afe5-3fd953e4f8f5/OceanDNA-b13475.fa]
[2023-03-16 20:47:18,784] [INFO] Query marker FASTA was written to OceanDNA-b13475/markers.fasta
[2023-03-16 20:47:18,785] [INFO] Task started: Blastn
[2023-03-16 20:47:18,785] [INFO] Running command: blastn -query OceanDNA-b13475/markers.fasta -db /var/lib/cwl/stg1707ed33-c30a-4a8a-87dc-bcef53c9334d/dqc_reference/reference_markers.fasta -out OceanDNA-b13475/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:19,283] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:19,284] [INFO] Selected 9 target genomes.
[2023-03-16 20:47:19,284] [INFO] Target genome list was writen to OceanDNA-b13475/target_genomes.txt
[2023-03-16 20:47:19,290] [INFO] Task started: fastANI
[2023-03-16 20:47:19,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfb33933-3a92-4a1a-afe5-3fd953e4f8f5/OceanDNA-b13475.fa --refList OceanDNA-b13475/target_genomes.txt --output OceanDNA-b13475/fastani_result.tsv --threads 1
[2023-03-16 20:47:22,646] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:22,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1707ed33-c30a-4a8a-87dc-bcef53c9334d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:47:22,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1707ed33-c30a-4a8a-87dc-bcef53c9334d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:47:22,653] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:47:22,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:47:22,653] [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
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.5782	145	414	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	78.5539	129	414	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.5266	155	414	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.425	151	414	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.9914	95	414	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	77.8858	84	414	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.8723	99	414	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	77.8626	105	414	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	77.6113	101	414	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:47:22,654] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13475/tc_result.tsv
[2023-03-16 20:47:22,654] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:47:22,654] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:47:22,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1707ed33-c30a-4a8a-87dc-bcef53c9334d/dqc_reference/checkm_data
[2023-03-16 20:47:22,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:47:22,658] [INFO] Task started: CheckM
[2023-03-16 20:47:22,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13475/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13475/checkm_input OceanDNA-b13475/checkm_result
[2023-03-16 20:47:45,350] [INFO] Task succeeded: CheckM
[2023-03-16 20:47:45,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:47:45,352] [INFO] ===== Completeness check finished =====
[2023-03-16 20:47:45,352] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:47:45,352] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13475/markers.fasta)
[2023-03-16 20:47:45,352] [INFO] Task started: Blastn
[2023-03-16 20:47:45,352] [INFO] Running command: blastn -query OceanDNA-b13475/markers.fasta -db /var/lib/cwl/stg1707ed33-c30a-4a8a-87dc-bcef53c9334d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13475/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:45,967] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:45,968] [INFO] Selected 12 target genomes.
[2023-03-16 20:47:45,968] [INFO] Target genome list was writen to OceanDNA-b13475/target_genomes_gtdb.txt
[2023-03-16 20:47:45,993] [INFO] Task started: fastANI
[2023-03-16 20:47:45,993] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfb33933-3a92-4a1a-afe5-3fd953e4f8f5/OceanDNA-b13475.fa --refList OceanDNA-b13475/target_genomes_gtdb.txt --output OceanDNA-b13475/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:47:50,663] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:50,671] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:47:50,671] [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_002781365.1	s__Sulfurimonas sp002781365	79.1065	148	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.89	0.98	0.96	19	-
GCA_001873135.1	s__Sulfurimonas sp001873135	78.8146	144	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391635.1	s__Sulfurimonas sp011391635	78.7347	128	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822665.1	s__Sulfurimonas sp018822665	78.7061	154	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCF_015265475.1	s__Sulfurimonas marisnigri	78.5782	145	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265455.1	s__Sulfurimonas baltica	78.5539	129	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242915.1	s__Sulfurimonas gotlandica	78.5266	155	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002732645.1	s__Sulfurimonas sp002732645	78.5101	75	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018825665.1	s__Sulfurimonas sp018825665	78.4448	128	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	0.97	0.97	2	-
GCA_016744025.1	s__Sulfurimonas sp016744025	78.184	125	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009883775.1	s__Sulfurimonas sp002452895	77.9328	105	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	-
GCA_001829715.1	s__Sulfurimonas sp001829715	77.7382	106	414	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:47:50,671] [INFO] GTDB search result was written to OceanDNA-b13475/result_gtdb.tsv
[2023-03-16 20:47:50,671] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:47:50,672] [INFO] DFAST_QC result json was written to OceanDNA-b13475/dqc_result.json
[2023-03-16 20:47:50,673] [INFO] DFAST_QC completed!
[2023-03-16 20:47:50,673] [INFO] Total running time: 0h0m40s