[2023-03-15 21:01:44,358] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,359] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,359] [INFO] DQC Reference Directory: /var/lib/cwl/stg79d49b30-601c-4a83-a26b-f0af369c343a/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,701] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,701] [INFO] Running command: cat /var/lib/cwl/stg6cd16394-cc63-4e3b-81d9-284349f7010e/OceanDNA-b31541.fa | prodigal -d OceanDNA-b31541/cds.fna -a OceanDNA-b31541/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:05,157] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:05,157] [INFO] Task started: HMMsearch
[2023-03-15 21:02:05,158] [INFO] Running command: hmmsearch --tblout OceanDNA-b31541/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79d49b30-601c-4a83-a26b-f0af369c343a/dqc_reference/reference_markers.hmm OceanDNA-b31541/protein.faa > /dev/null
[2023-03-15 21:02:05,352] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:05,352] [INFO] Found 6/6 markers.
[2023-03-15 21:02:05,371] [INFO] Query marker FASTA was written to OceanDNA-b31541/markers.fasta
[2023-03-15 21:02:05,372] [INFO] Task started: Blastn
[2023-03-15 21:02:05,372] [INFO] Running command: blastn -query OceanDNA-b31541/markers.fasta -db /var/lib/cwl/stg79d49b30-601c-4a83-a26b-f0af369c343a/dqc_reference/reference_markers.fasta -out OceanDNA-b31541/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:06,153] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:06,154] [INFO] Selected 21 target genomes.
[2023-03-15 21:02:06,154] [INFO] Target genome list was writen to OceanDNA-b31541/target_genomes.txt
[2023-03-15 21:02:06,167] [INFO] Task started: fastANI
[2023-03-15 21:02:06,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cd16394-cc63-4e3b-81d9-284349f7010e/OceanDNA-b31541.fa --refList OceanDNA-b31541/target_genomes.txt --output OceanDNA-b31541/fastani_result.tsv --threads 1
[2023-03-15 21:02:17,912] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:17,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79d49b30-601c-4a83-a26b-f0af369c343a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:17,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79d49b30-601c-4a83-a26b-f0af369c343a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:17,924] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:17,924] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:17,924] [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
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	84.1842	699	1022	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	79.0485	397	1022	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.2169	367	1022	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.1764	300	1022	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.0539	342	1022	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	77.94	323	1022	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.9327	294	1022	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	77.9258	283	1022	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	77.9226	284	1022	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.8908	323	1022	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	77.8506	275	1022	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	77.8153	274	1022	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	77.8113	257	1022	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	77.8064	271	1022	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.7895	269	1022	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	77.7819	275	1022	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	77.7763	252	1022	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.7269	293	1022	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	77.7089	274	1022	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	77.5751	260	1022	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	77.0786	180	1022	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:17,925] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31541/tc_result.tsv
[2023-03-15 21:02:17,925] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:17,925] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:17,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79d49b30-601c-4a83-a26b-f0af369c343a/dqc_reference/checkm_data
[2023-03-15 21:02:17,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:17,930] [INFO] Task started: CheckM
[2023-03-15 21:02:17,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31541/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31541/checkm_input OceanDNA-b31541/checkm_result
[2023-03-15 21:03:06,412] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:06,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:06,415] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:06,415] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:06,415] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31541/markers.fasta)
[2023-03-15 21:03:06,417] [INFO] Task started: Blastn
[2023-03-15 21:03:06,417] [INFO] Running command: blastn -query OceanDNA-b31541/markers.fasta -db /var/lib/cwl/stg79d49b30-601c-4a83-a26b-f0af369c343a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31541/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:07,871] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:07,872] [INFO] Selected 20 target genomes.
[2023-03-15 21:03:07,872] [INFO] Target genome list was writen to OceanDNA-b31541/target_genomes_gtdb.txt
[2023-03-15 21:03:08,168] [INFO] Task started: fastANI
[2023-03-15 21:03:08,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cd16394-cc63-4e3b-81d9-284349f7010e/OceanDNA-b31541.fa --refList OceanDNA-b31541/target_genomes_gtdb.txt --output OceanDNA-b31541/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:19,154] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:19,165] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:03:19,165] [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_009828115.1	s__Pseudopontixanthobacter_A sediminis	84.1738	700	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	79.0464	396	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.2872	382	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.2794	347	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.235	337	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.2169	367	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.1547	300	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979275.1	s__Pseudopontixanthobacter vadosimaris	78.0583	337	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898545.1	s__Caenibius sp001898545	77.952	241	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828095.1	s__Pontixanthobacter luteolus	77.94	323	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	77.9194	291	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_002278985.1	s__34-65-8 sp002278985	77.8887	197	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__34-65-8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	77.8488	246	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827395.1	s__Pontixanthobacter aquaemixtae	77.8481	274	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	77.8429	298	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	77.8297	291	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCA_003248395.1	s__Qipengyuania sp003248395	77.745	239	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911835.1	s__Erythrobacter sp013911835	77.7103	195	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605755.1	s__Tsuneonella suprasediminis	77.5595	235	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	77.5117	271	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:19,165] [INFO] GTDB search result was written to OceanDNA-b31541/result_gtdb.tsv
[2023-03-15 21:03:19,165] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:19,167] [INFO] DFAST_QC result json was written to OceanDNA-b31541/dqc_result.json
[2023-03-15 21:03:19,167] [INFO] DFAST_QC completed!
[2023-03-15 21:03:19,168] [INFO] Total running time: 0h1m35s