[2023-03-16 08:50:59,669] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:59,670] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:59,670] [INFO] DQC Reference Directory: /var/lib/cwl/stgb763db4f-19ff-4124-a16e-5fa7b001ed15/dqc_reference
[2023-03-16 08:51:00,871] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,872] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,872] [INFO] Running command: cat /var/lib/cwl/stg432a5397-b675-4635-9ece-2ad56bc42754/OceanDNA-b28203.fa | prodigal -d OceanDNA-b28203/cds.fna -a OceanDNA-b28203/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:25,966] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:25,966] [INFO] Task started: HMMsearch
[2023-03-16 08:51:25,966] [INFO] Running command: hmmsearch --tblout OceanDNA-b28203/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb763db4f-19ff-4124-a16e-5fa7b001ed15/dqc_reference/reference_markers.hmm OceanDNA-b28203/protein.faa > /dev/null
[2023-03-16 08:51:26,213] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:26,214] [INFO] Found 6/6 markers.
[2023-03-16 08:51:26,244] [INFO] Query marker FASTA was written to OceanDNA-b28203/markers.fasta
[2023-03-16 08:51:26,244] [INFO] Task started: Blastn
[2023-03-16 08:51:26,245] [INFO] Running command: blastn -query OceanDNA-b28203/markers.fasta -db /var/lib/cwl/stgb763db4f-19ff-4124-a16e-5fa7b001ed15/dqc_reference/reference_markers.fasta -out OceanDNA-b28203/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:27,220] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:27,223] [INFO] Selected 30 target genomes.
[2023-03-16 08:51:27,223] [INFO] Target genome list was writen to OceanDNA-b28203/target_genomes.txt
[2023-03-16 08:51:27,254] [INFO] Task started: fastANI
[2023-03-16 08:51:27,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg432a5397-b675-4635-9ece-2ad56bc42754/OceanDNA-b28203.fa --refList OceanDNA-b28203/target_genomes.txt --output OceanDNA-b28203/fastani_result.tsv --threads 1
[2023-03-16 08:51:50,367] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:50,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb763db4f-19ff-4124-a16e-5fa7b001ed15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:50,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb763db4f-19ff-4124-a16e-5fa7b001ed15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:50,390] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:50,390] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:51:50,390] [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
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.4371	576	1292	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.9552	520	1292	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.8351	559	1292	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.8278	578	1292	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.8089	359	1292	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.7943	485	1292	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.7921	569	1292	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	78.674	492	1292	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.6476	401	1292	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.6055	496	1292	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.6019	463	1292	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5815	441	1292	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.541	458	1292	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.3627	441	1292	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	78.3421	481	1292	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.3307	435	1292	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	78.2844	396	1292	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.2593	402	1292	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.241	439	1292	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.1661	433	1292	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.1228	434	1292	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	78.0696	403	1292	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.0242	403	1292	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	78.0038	393	1292	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	78.0005	388	1292	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.9981	406	1292	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.9431	375	1292	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.9118	408	1292	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.814	444	1292	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	77.5396	347	1292	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:51:50,391] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28203/tc_result.tsv
[2023-03-16 08:51:50,395] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:50,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:50,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb763db4f-19ff-4124-a16e-5fa7b001ed15/dqc_reference/checkm_data
[2023-03-16 08:51:50,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:50,404] [INFO] Task started: CheckM
[2023-03-16 08:51:50,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28203/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28203/checkm_input OceanDNA-b28203/checkm_result
[2023-03-16 08:52:59,577] [INFO] Task succeeded: CheckM
[2023-03-16 08:52:59,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:52:59,600] [INFO] ===== Completeness check finished =====
[2023-03-16 08:52:59,600] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:52:59,600] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28203/markers.fasta)
[2023-03-16 08:52:59,601] [INFO] Task started: Blastn
[2023-03-16 08:52:59,601] [INFO] Running command: blastn -query OceanDNA-b28203/markers.fasta -db /var/lib/cwl/stgb763db4f-19ff-4124-a16e-5fa7b001ed15/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28203/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:53:01,471] [INFO] Task succeeded: Blastn
[2023-03-16 08:53:01,473] [INFO] Selected 24 target genomes.
[2023-03-16 08:53:01,473] [INFO] Target genome list was writen to OceanDNA-b28203/target_genomes_gtdb.txt
[2023-03-16 08:53:01,521] [INFO] Task started: fastANI
[2023-03-16 08:53:01,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg432a5397-b675-4635-9ece-2ad56bc42754/OceanDNA-b28203.fa --refList OceanDNA-b28203/target_genomes_gtdb.txt --output OceanDNA-b28203/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:53:20,431] [INFO] Task succeeded: fastANI
[2023-03-16 08:53:20,445] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:53:20,446] [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_001650895.1	s__EhC02 sp001650895	91.2706	1062	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282555.1	s__EhC02 sp002282555	83.5278	399	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.6028	661	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009857745.1	s__Thalassobius mangrovi	79.4459	575	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	79.1031	546	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	78.8609	466	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.8305	559	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	78.8199	454	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900129345.1	s__Ruegeria intermedia	78.778	488	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.7525	527	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	78.7421	558	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.7415	491	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	78.6704	357	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	78.6201	461	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.5728	515	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.4386	462	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	78.4108	462	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125575.1	s__JAACUH01 sp016125575	78.3337	402	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	78.3044	450	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000382265.1	s__Yoonia vestfoldensis	78.3036	394	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	78.2514	437	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_001620265.1	s__Frigidibacter mobilis	78.2404	439	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	78.1462	436	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_015223355.1	s__Salipiger pacificus_B	78.0756	452	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:53:20,447] [INFO] GTDB search result was written to OceanDNA-b28203/result_gtdb.tsv
[2023-03-16 08:53:20,447] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:53:20,451] [INFO] DFAST_QC result json was written to OceanDNA-b28203/dqc_result.json
[2023-03-16 08:53:20,451] [INFO] DFAST_QC completed!
[2023-03-16 08:53:20,451] [INFO] Total running time: 0h2m21s