[2023-03-14 10:56:00,305] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:56:00,306] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:56:00,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg497b7dca-77f1-4b62-b9cc-720273fc9d4f/dqc_reference
[2023-03-14 10:56:01,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:01,461] [INFO] Task started: Prodigal
[2023-03-14 10:56:01,461] [INFO] Running command: cat /var/lib/cwl/stg4e1465af-728f-406a-b13f-09eb27111f33/OceanDNA-b26640.fa | prodigal -d OceanDNA-b26640/cds.fna -a OceanDNA-b26640/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:29,296] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:29,296] [INFO] Task started: HMMsearch
[2023-03-14 10:56:29,296] [INFO] Running command: hmmsearch --tblout OceanDNA-b26640/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg497b7dca-77f1-4b62-b9cc-720273fc9d4f/dqc_reference/reference_markers.hmm OceanDNA-b26640/protein.faa > /dev/null
[2023-03-14 10:56:29,626] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:29,626] [INFO] Found 6/6 markers.
[2023-03-14 10:56:29,658] [INFO] Query marker FASTA was written to OceanDNA-b26640/markers.fasta
[2023-03-14 10:56:29,658] [INFO] Task started: Blastn
[2023-03-14 10:56:29,658] [INFO] Running command: blastn -query OceanDNA-b26640/markers.fasta -db /var/lib/cwl/stg497b7dca-77f1-4b62-b9cc-720273fc9d4f/dqc_reference/reference_markers.fasta -out OceanDNA-b26640/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:30,453] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:30,454] [INFO] Selected 14 target genomes.
[2023-03-14 10:56:30,454] [INFO] Target genome list was writen to OceanDNA-b26640/target_genomes.txt
[2023-03-14 10:56:30,463] [INFO] Task started: fastANI
[2023-03-14 10:56:30,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e1465af-728f-406a-b13f-09eb27111f33/OceanDNA-b26640.fa --refList OceanDNA-b26640/target_genomes.txt --output OceanDNA-b26640/fastani_result.tsv --threads 1
[2023-03-14 10:56:43,020] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:43,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg497b7dca-77f1-4b62-b9cc-720273fc9d4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:43,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg497b7dca-77f1-4b62-b9cc-720273fc9d4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:43,030] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:43,030] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:43,030] [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
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	78.8929	540	1421	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	78.817	525	1421	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	78.3233	481	1421	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	78.2953	477	1421	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	78.2795	540	1421	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.4889	219	1421	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.3248	189	1421	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.2305	112	1421	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	76.1791	209	1421	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.9807	194	1421	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	75.9645	187	1421	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	75.9549	132	1421	95	below_threshold
Fulvimarina pelagi	strain=DSM 15513	GCA_001463845.1	217511	217511	type	True	75.8764	104	1421	95	below_threshold
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	75.8637	105	1421	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:43,031] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26640/tc_result.tsv
[2023-03-14 10:56:43,031] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:43,031] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:43,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg497b7dca-77f1-4b62-b9cc-720273fc9d4f/dqc_reference/checkm_data
[2023-03-14 10:56:43,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:43,038] [INFO] Task started: CheckM
[2023-03-14 10:56:43,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26640/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26640/checkm_input OceanDNA-b26640/checkm_result
[2023-03-14 10:57:54,442] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:54,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:54,445] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:54,445] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:54,445] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26640/markers.fasta)
[2023-03-14 10:57:54,445] [INFO] Task started: Blastn
[2023-03-14 10:57:54,445] [INFO] Running command: blastn -query OceanDNA-b26640/markers.fasta -db /var/lib/cwl/stg497b7dca-77f1-4b62-b9cc-720273fc9d4f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26640/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:55,789] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:55,790] [INFO] Selected 21 target genomes.
[2023-03-14 10:57:55,790] [INFO] Target genome list was writen to OceanDNA-b26640/target_genomes_gtdb.txt
[2023-03-14 10:57:55,808] [INFO] Task started: fastANI
[2023-03-14 10:57:55,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e1465af-728f-406a-b13f-09eb27111f33/OceanDNA-b26640.fa --refList OceanDNA-b26640/target_genomes_gtdb.txt --output OceanDNA-b26640/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:58:14,648] [INFO] Task succeeded: fastANI
[2023-03-14 10:58:14,659] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:58:14,660] [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
GCF_003258595.1	s__Acuticoccus sediminis	78.8792	543	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016411865.1	s__Acuticoccus sp016411865	78.829	523	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927245.1	s__Acuticoccus yangtzensis	78.3003	483	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	98.76	97.53	0.97	0.95	3	-
GCF_003258835.1	s__Rhodobium orientis	76.8825	234	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_000374525.1	s__Amorphus coralli	76.8796	256	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	76.5891	270	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	76.5885	203	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_014050225.1	s__Hongsoonwoonella albiluteola	76.5835	159	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148505.1	s__Pseudoxanthobacter soli	76.4575	237	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	76.4547	210	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	76.4039	241	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281615.1	s__Rhodoligotrophos sp005281615	76.2254	111	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046185.1	s__Phreatobacter oligotrophus	76.203	203	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	76.1241	227	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653355.1	s__Rhodoplanes elegans	75.9842	220	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_003258865.1	s__Rhodoplanes roseus	75.9757	198	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137085.1	s__Lichenihabitans ramalinae	75.9648	187	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153705.1	s__Fulvimarina pelagi	75.8637	105	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013377085.1	s__Rhodoplanes sp013377085	75.769	230	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241425.1	s__JAFAXA01 sp019241425	75.4555	77	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAXA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:58:14,660] [INFO] GTDB search result was written to OceanDNA-b26640/result_gtdb.tsv
[2023-03-14 10:58:14,660] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:58:14,662] [INFO] DFAST_QC result json was written to OceanDNA-b26640/dqc_result.json
[2023-03-14 10:58:14,662] [INFO] DFAST_QC completed!
[2023-03-14 10:58:14,662] [INFO] Total running time: 0h2m14s