[2023-03-15 06:03:50,833] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:03:50,833] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:03:50,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg254a9f4e-febb-4e35-a82d-b2d14f9707d3/dqc_reference
[2023-03-15 06:03:51,922] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:03:51,922] [INFO] Task started: Prodigal
[2023-03-15 06:03:51,923] [INFO] Running command: cat /var/lib/cwl/stg0f20c199-9291-4aa9-9621-67e9325988a7/OceanDNA-b28158.fa | prodigal -d OceanDNA-b28158/cds.fna -a OceanDNA-b28158/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:04:11,656] [INFO] Task succeeded: Prodigal
[2023-03-15 06:04:11,656] [INFO] Task started: HMMsearch
[2023-03-15 06:04:11,656] [INFO] Running command: hmmsearch --tblout OceanDNA-b28158/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg254a9f4e-febb-4e35-a82d-b2d14f9707d3/dqc_reference/reference_markers.hmm OceanDNA-b28158/protein.faa > /dev/null
[2023-03-15 06:04:11,849] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:04:11,850] [INFO] Found 6/6 markers.
[2023-03-15 06:04:11,872] [INFO] Query marker FASTA was written to OceanDNA-b28158/markers.fasta
[2023-03-15 06:04:11,873] [INFO] Task started: Blastn
[2023-03-15 06:04:11,873] [INFO] Running command: blastn -query OceanDNA-b28158/markers.fasta -db /var/lib/cwl/stg254a9f4e-febb-4e35-a82d-b2d14f9707d3/dqc_reference/reference_markers.fasta -out OceanDNA-b28158/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:04:12,805] [INFO] Task succeeded: Blastn
[2023-03-15 06:04:12,806] [INFO] Selected 26 target genomes.
[2023-03-15 06:04:12,806] [INFO] Target genome list was writen to OceanDNA-b28158/target_genomes.txt
[2023-03-15 06:04:12,821] [INFO] Task started: fastANI
[2023-03-15 06:04:12,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f20c199-9291-4aa9-9621-67e9325988a7/OceanDNA-b28158.fa --refList OceanDNA-b28158/target_genomes.txt --output OceanDNA-b28158/fastani_result.tsv --threads 1
[2023-03-15 06:04:30,298] [INFO] Task succeeded: fastANI
[2023-03-15 06:04:30,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg254a9f4e-febb-4e35-a82d-b2d14f9707d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:04:30,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg254a9f4e-febb-4e35-a82d-b2d14f9707d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:04:30,313] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:04:30,313] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:04:30,313] [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
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	79.8407	493	1054	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	79.6176	469	1054	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	79.5922	433	1054	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.5724	470	1054	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	79.5373	439	1054	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	79.5216	480	1054	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	79.3127	475	1054	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.2182	474	1054	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.1652	489	1054	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	79.0761	421	1054	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	79.0752	383	1054	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	79.0439	429	1054	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.7713	382	1054	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.7392	302	1054	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.7106	416	1054	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.6437	360	1054	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.6216	461	1054	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	78.6215	367	1054	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	78.5186	372	1054	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.4839	367	1054	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	78.3596	355	1054	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.3395	364	1054	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.0997	375	1054	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.062	339	1054	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.9031	289	1054	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.675	318	1054	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:04:30,313] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28158/tc_result.tsv
[2023-03-15 06:04:30,313] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:04:30,313] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:04:30,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg254a9f4e-febb-4e35-a82d-b2d14f9707d3/dqc_reference/checkm_data
[2023-03-15 06:04:30,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:04:30,319] [INFO] Task started: CheckM
[2023-03-15 06:04:30,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28158/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28158/checkm_input OceanDNA-b28158/checkm_result
[2023-03-15 06:05:21,352] [INFO] Task succeeded: CheckM
[2023-03-15 06:05:21,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.76%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:05:21,386] [INFO] ===== Completeness check finished =====
[2023-03-15 06:05:21,386] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:05:21,386] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28158/markers.fasta)
[2023-03-15 06:05:21,387] [INFO] Task started: Blastn
[2023-03-15 06:05:21,387] [INFO] Running command: blastn -query OceanDNA-b28158/markers.fasta -db /var/lib/cwl/stg254a9f4e-febb-4e35-a82d-b2d14f9707d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28158/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:05:23,246] [INFO] Task succeeded: Blastn
[2023-03-15 06:05:23,257] [INFO] Selected 21 target genomes.
[2023-03-15 06:05:23,257] [INFO] Target genome list was writen to OceanDNA-b28158/target_genomes_gtdb.txt
[2023-03-15 06:05:23,278] [INFO] Task started: fastANI
[2023-03-15 06:05:23,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f20c199-9291-4aa9-9621-67e9325988a7/OceanDNA-b28158.fa --refList OceanDNA-b28158/target_genomes_gtdb.txt --output OceanDNA-b28158/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:05:38,715] [INFO] Task succeeded: fastANI
[2023-03-15 06:05:38,727] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:05:38,727] [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_014196965.1	s__Actibacterium_A naphthalenivorans	97.6165	994	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	conclusive
GCF_018139985.1	s__JAGSOU01 sp018139985	81.1339	541	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	80.5093	576	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278325.1	s__JADQCB01 sp016278325	79.9876	453	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	79.9566	487	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	79.8482	541	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	79.8189	495	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	79.5317	479	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	79.5032	442	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004342445.1	s__Rhodovulum euryhalinum	79.337	474	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	79.2662	474	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_009857745.1	s__Thalassobius mangrovi	79.1454	491	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000647975.1	s__Actibacterium mucosum	79.0754	383	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106675.1	s__Acidimangrovimonas indica	79.0492	428	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_900142935.1	s__Rhodovulum sp900142935	79.0213	460	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124615.1	s__Solirhodobacter sp016124615	78.791	443	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	78.7208	415	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.6673	358	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCA_019061145.1	s__ASV31 sp019061145	78.6356	386	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	78.3134	385	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	77.497	186	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:05:38,729] [INFO] GTDB search result was written to OceanDNA-b28158/result_gtdb.tsv
[2023-03-15 06:05:38,733] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:05:38,738] [INFO] DFAST_QC result json was written to OceanDNA-b28158/dqc_result.json
[2023-03-15 06:05:38,738] [INFO] DFAST_QC completed!
[2023-03-15 06:05:38,738] [INFO] Total running time: 0h1m48s