[2023-03-18 01:43:46,123] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:43:46,125] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:43:46,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg1273f28c-4f11-4589-8009-197c1cf49b8c/dqc_reference
[2023-03-18 01:43:47,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:43:47,229] [INFO] Task started: Prodigal
[2023-03-18 01:43:47,229] [INFO] Running command: cat /var/lib/cwl/stgc07c24f3-78d4-4fd0-b0c8-afe1b4546142/OceanDNA-b31691.fa | prodigal -d OceanDNA-b31691/cds.fna -a OceanDNA-b31691/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:43:54,922] [INFO] Task succeeded: Prodigal
[2023-03-18 01:43:54,923] [INFO] Task started: HMMsearch
[2023-03-18 01:43:54,923] [INFO] Running command: hmmsearch --tblout OceanDNA-b31691/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1273f28c-4f11-4589-8009-197c1cf49b8c/dqc_reference/reference_markers.hmm OceanDNA-b31691/protein.faa > /dev/null
[2023-03-18 01:43:55,077] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:43:55,077] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc07c24f3-78d4-4fd0-b0c8-afe1b4546142/OceanDNA-b31691.fa]
[2023-03-18 01:43:55,102] [INFO] Query marker FASTA was written to OceanDNA-b31691/markers.fasta
[2023-03-18 01:43:55,104] [INFO] Task started: Blastn
[2023-03-18 01:43:55,104] [INFO] Running command: blastn -query OceanDNA-b31691/markers.fasta -db /var/lib/cwl/stg1273f28c-4f11-4589-8009-197c1cf49b8c/dqc_reference/reference_markers.fasta -out OceanDNA-b31691/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:43:55,777] [INFO] Task succeeded: Blastn
[2023-03-18 01:43:55,782] [INFO] Selected 31 target genomes.
[2023-03-18 01:43:55,782] [INFO] Target genome list was writen to OceanDNA-b31691/target_genomes.txt
[2023-03-18 01:43:55,801] [INFO] Task started: fastANI
[2023-03-18 01:43:55,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07c24f3-78d4-4fd0-b0c8-afe1b4546142/OceanDNA-b31691.fa --refList OceanDNA-b31691/target_genomes.txt --output OceanDNA-b31691/fastani_result.tsv --threads 1
[2023-03-18 01:44:11,525] [INFO] Task succeeded: fastANI
[2023-03-18 01:44:11,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1273f28c-4f11-4589-8009-197c1cf49b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:44:11,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1273f28c-4f11-4589-8009-197c1cf49b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:44:11,541] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:44:11,541] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:44:11,542] [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
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	77.6905	150	374	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.6266	108	374	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	77.6056	118	374	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	77.5967	134	374	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.5948	137	374	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.5911	140	374	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.5644	153	374	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.4919	151	374	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	77.4052	126	374	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.3527	137	374	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	77.3408	123	374	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.2659	124	374	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	77.2574	142	374	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.2389	121	374	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	77.2371	141	374	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	77.0064	82	374	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	76.9757	128	374	95	below_threshold
Croceicoccus pelagius	strain=CGMCC 1.15358	GCA_014642495.1	1703341	1703341	type	True	76.9742	84	374	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	76.8851	105	374	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	76.8611	98	374	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	76.8303	102	374	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	76.8211	106	374	95	below_threshold
Aurantiacibacter arachoides	strain=RC4-10-4	GCA_009827335.1	1850444	1850444	type	True	76.7891	110	374	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	76.7245	112	374	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	76.4741	100	374	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	76.4725	77	374	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	76.2306	80	374	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	76.1741	80	374	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	76.1581	75	374	95	below_threshold
Caenibius tardaugens	strain=NBRC 16725	GCA_003860345.1	169176	169176	type	True	75.9475	63	374	95	below_threshold
Caenibius tardaugens	strain=NBRC 16725	GCA_000466945.1	169176	169176	type	True	75.9475	63	374	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:44:11,545] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31691/tc_result.tsv
[2023-03-18 01:44:11,547] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:44:11,547] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:44:11,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1273f28c-4f11-4589-8009-197c1cf49b8c/dqc_reference/checkm_data
[2023-03-18 01:44:11,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:44:11,571] [INFO] Task started: CheckM
[2023-03-18 01:44:11,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31691/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31691/checkm_input OceanDNA-b31691/checkm_result
[2023-03-18 01:44:35,593] [INFO] Task succeeded: CheckM
[2023-03-18 01:44:35,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:44:35,631] [INFO] ===== Completeness check finished =====
[2023-03-18 01:44:35,631] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:44:35,632] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31691/markers.fasta)
[2023-03-18 01:44:35,633] [INFO] Task started: Blastn
[2023-03-18 01:44:35,633] [INFO] Running command: blastn -query OceanDNA-b31691/markers.fasta -db /var/lib/cwl/stg1273f28c-4f11-4589-8009-197c1cf49b8c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31691/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:36,795] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:36,800] [INFO] Selected 28 target genomes.
[2023-03-18 01:44:36,800] [INFO] Target genome list was writen to OceanDNA-b31691/target_genomes_gtdb.txt
[2023-03-18 01:44:36,831] [INFO] Task started: fastANI
[2023-03-18 01:44:36,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07c24f3-78d4-4fd0-b0c8-afe1b4546142/OceanDNA-b31691.fa --refList OceanDNA-b31691/target_genomes_gtdb.txt --output OceanDNA-b31691/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:44:50,349] [INFO] Task succeeded: fastANI
[2023-03-18 01:44:50,365] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:44:50,365] [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_009993605.1	s__Qipengyuania sp009993605	77.9911	149	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	77.7754	155	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	77.7322	149	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_009827315.1	s__Qipengyuania gaetbuli	77.7127	149	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	77.681	134	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	77.5911	140	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	77.5522	136	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	77.482	151	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	77.4811	133	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	77.407	146	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	77.3742	136	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	77.3712	148	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	77.2889	123	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719165.1	s__Erythrobacter litoralis	77.2574	142	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001542855.1	s__Qipengyuania sp001542855	77.2405	132	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	77.1676	95	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793865.1	s__Qipengyuania sp016793865	77.0278	99	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363635.1	s__Erythrobacter sp009363635	76.9337	107	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698205.1	s__Tsuneonella dongtanensis	76.8902	108	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358425.1	s__Qipengyuania sediminis	76.8421	92	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	76.8375	107	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_014644315.1	s__Tsuneonella deserti	76.8366	99	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	76.7081	95	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745095.1	s__Croceicoccus sp016745095	76.6661	95	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152865.1	s__Erythrobacter sp000152865	76.6575	104	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230355.1	s__Novosphingobium piscinae	76.4806	78	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707465.1	s__Novosphingobium sp009707465	76.4171	85	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842735.1	s__Erythrobacter sp002842735	76.3897	91	374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	95.33	95.33	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:44:50,367] [INFO] GTDB search result was written to OceanDNA-b31691/result_gtdb.tsv
[2023-03-18 01:44:50,367] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:44:50,372] [INFO] DFAST_QC result json was written to OceanDNA-b31691/dqc_result.json
[2023-03-18 01:44:50,372] [INFO] DFAST_QC completed!
[2023-03-18 01:44:50,372] [INFO] Total running time: 0h1m4s