[2023-03-16 18:55:24,747] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:55:24,747] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:55:24,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg5692c468-930e-4596-8f59-f413970a057e/dqc_reference
[2023-03-16 18:55:26,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:55:26,451] [INFO] Task started: Prodigal
[2023-03-16 18:55:26,451] [INFO] Running command: cat /var/lib/cwl/stg04ddc9aa-b1d8-47f4-81cf-e1c00cd3b497/OceanDNA-b29598.fa | prodigal -d OceanDNA-b29598/cds.fna -a OceanDNA-b29598/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:55:46,528] [INFO] Task succeeded: Prodigal
[2023-03-16 18:55:46,528] [INFO] Task started: HMMsearch
[2023-03-16 18:55:46,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b29598/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5692c468-930e-4596-8f59-f413970a057e/dqc_reference/reference_markers.hmm OceanDNA-b29598/protein.faa > /dev/null
[2023-03-16 18:55:46,727] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:55:46,727] [INFO] Found 6/6 markers.
[2023-03-16 18:55:46,864] [INFO] Query marker FASTA was written to OceanDNA-b29598/markers.fasta
[2023-03-16 18:55:46,865] [INFO] Task started: Blastn
[2023-03-16 18:55:46,865] [INFO] Running command: blastn -query OceanDNA-b29598/markers.fasta -db /var/lib/cwl/stg5692c468-930e-4596-8f59-f413970a057e/dqc_reference/reference_markers.fasta -out OceanDNA-b29598/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:55:47,730] [INFO] Task succeeded: Blastn
[2023-03-16 18:55:47,733] [INFO] Selected 18 target genomes.
[2023-03-16 18:55:47,733] [INFO] Target genome list was writen to OceanDNA-b29598/target_genomes.txt
[2023-03-16 18:55:47,778] [INFO] Task started: fastANI
[2023-03-16 18:55:47,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg04ddc9aa-b1d8-47f4-81cf-e1c00cd3b497/OceanDNA-b29598.fa --refList OceanDNA-b29598/target_genomes.txt --output OceanDNA-b29598/fastani_result.tsv --threads 1
[2023-03-16 18:56:10,327] [INFO] Task succeeded: fastANI
[2023-03-16 18:56:10,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5692c468-930e-4596-8f59-f413970a057e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:56:10,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5692c468-930e-4596-8f59-f413970a057e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:56:10,339] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:56:10,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:56:10,339] [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
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	82.5984	683	1075	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	82.5339	654	1075	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.7572	639	1075	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.7499	622	1075	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	81.6343	589	1075	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	81.5661	618	1075	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	81.5643	607	1075	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	81.5593	626	1075	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	81.4864	659	1075	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	81.4785	609	1075	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	81.4114	614	1075	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	81.383	622	1075	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.1773	617	1075	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	81.1234	608	1075	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	81.0983	618	1075	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.8313	574	1075	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	79.9594	541	1075	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.7284	552	1075	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:56:10,340] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29598/tc_result.tsv
[2023-03-16 18:56:10,340] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:56:10,340] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:56:10,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5692c468-930e-4596-8f59-f413970a057e/dqc_reference/checkm_data
[2023-03-16 18:56:10,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:56:10,416] [INFO] Task started: CheckM
[2023-03-16 18:56:10,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29598/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29598/checkm_input OceanDNA-b29598/checkm_result
[2023-03-16 18:57:18,847] [INFO] Task succeeded: CheckM
[2023-03-16 18:57:18,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:57:18,851] [INFO] ===== Completeness check finished =====
[2023-03-16 18:57:18,851] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:57:18,851] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29598/markers.fasta)
[2023-03-16 18:57:18,852] [INFO] Task started: Blastn
[2023-03-16 18:57:18,852] [INFO] Running command: blastn -query OceanDNA-b29598/markers.fasta -db /var/lib/cwl/stg5692c468-930e-4596-8f59-f413970a057e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29598/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:57:20,324] [INFO] Task succeeded: Blastn
[2023-03-16 18:57:20,328] [INFO] Selected 13 target genomes.
[2023-03-16 18:57:20,328] [INFO] Target genome list was writen to OceanDNA-b29598/target_genomes_gtdb.txt
[2023-03-16 18:57:20,363] [INFO] Task started: fastANI
[2023-03-16 18:57:20,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg04ddc9aa-b1d8-47f4-81cf-e1c00cd3b497/OceanDNA-b29598.fa --refList OceanDNA-b29598/target_genomes_gtdb.txt --output OceanDNA-b29598/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:57:30,815] [INFO] Task succeeded: fastANI
[2023-03-16 18:57:30,823] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:57:30,823] [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_002294185.1	s__Paracoccus sp002294185	99.7492	996	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	conclusive
GCF_018860165.1	s__Paracoccus sp018860165	82.6633	671	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	82.5731	686	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900631945.1	s__Paracoccus haematequi	81.9577	644	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744015.1	s__Paracoccus sp002732665	81.9327	690	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_017315735.1	s__Paracoccus sp017315735	81.7694	620	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642735.1	s__Paracoccus acridae	81.5702	625	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_900110285.1	s__Paracoccus alcaliphilus	81.5573	609	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111675.1	s__Paracoccus homiensis	81.4863	658	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188295.1	s__Paracoccus sediminis	81.1082	616	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003337565.1	s__Paracoccus lutimaris	79.9431	543	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847305.1	s__Paracoccus sp002847305	79.7094	553	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056045.1	s__Paracoccus sp018056045	79.5021	354	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:57:30,825] [INFO] GTDB search result was written to OceanDNA-b29598/result_gtdb.tsv
[2023-03-16 18:57:30,827] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:57:30,830] [INFO] DFAST_QC result json was written to OceanDNA-b29598/dqc_result.json
[2023-03-16 18:57:30,830] [INFO] DFAST_QC completed!
[2023-03-16 18:57:30,830] [INFO] Total running time: 0h2m6s