[2023-03-18 09:58:36,586] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:58:36,586] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:58:36,586] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdfbd02c-eaaf-46e7-96ce-77b1536e01aa/dqc_reference
[2023-03-18 09:58:38,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:58:38,404] [INFO] Task started: Prodigal
[2023-03-18 09:58:38,404] [INFO] Running command: cat /var/lib/cwl/stgd35a4e38-a5aa-407c-a381-dd72ab2c78f9/OceanDNA-b32019.fa | prodigal -d OceanDNA-b32019/cds.fna -a OceanDNA-b32019/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:58:54,837] [INFO] Task succeeded: Prodigal
[2023-03-18 09:58:54,837] [INFO] Task started: HMMsearch
[2023-03-18 09:58:54,837] [INFO] Running command: hmmsearch --tblout OceanDNA-b32019/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdfbd02c-eaaf-46e7-96ce-77b1536e01aa/dqc_reference/reference_markers.hmm OceanDNA-b32019/protein.faa > /dev/null
[2023-03-18 09:58:55,090] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:58:55,091] [INFO] Found 6/6 markers.
[2023-03-18 09:58:55,110] [INFO] Query marker FASTA was written to OceanDNA-b32019/markers.fasta
[2023-03-18 09:58:55,110] [INFO] Task started: Blastn
[2023-03-18 09:58:55,110] [INFO] Running command: blastn -query OceanDNA-b32019/markers.fasta -db /var/lib/cwl/stgcdfbd02c-eaaf-46e7-96ce-77b1536e01aa/dqc_reference/reference_markers.fasta -out OceanDNA-b32019/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:58:55,896] [INFO] Task succeeded: Blastn
[2023-03-18 09:58:55,897] [INFO] Selected 31 target genomes.
[2023-03-18 09:58:55,897] [INFO] Target genome list was writen to OceanDNA-b32019/target_genomes.txt
[2023-03-18 09:58:55,923] [INFO] Task started: fastANI
[2023-03-18 09:58:55,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgd35a4e38-a5aa-407c-a381-dd72ab2c78f9/OceanDNA-b32019.fa --refList OceanDNA-b32019/target_genomes.txt --output OceanDNA-b32019/fastani_result.tsv --threads 1
[2023-03-18 09:59:14,423] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:14,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdfbd02c-eaaf-46e7-96ce-77b1536e01aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:59:14,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdfbd02c-eaaf-46e7-96ce-77b1536e01aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:59:14,440] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:59:14,440] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:59:14,440] [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
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.7806	202	867	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.6469	310	867	95	below_threshold
Caenibius tardaugens	strain=NBRC 16725	GCA_003860345.1	169176	169176	type	True	78.639	327	867	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.636	312	867	95	below_threshold
Caenibius tardaugens	strain=NBRC 16725	GCA_000466945.1	169176	169176	type	True	78.59	326	867	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.5628	334	867	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.5	274	867	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	78.4162	329	867	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	78.4006	313	867	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.3648	264	867	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	78.3304	200	867	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.2251	216	867	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.1913	245	867	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.1553	273	867	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	78.1202	254	867	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.1066	283	867	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	78.0751	270	867	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.044	243	867	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.0135	228	867	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	77.9526	241	867	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	77.8893	226	867	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	77.8763	224	867	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	77.8715	230	867	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	77.8664	211	867	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	77.8525	212	867	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	77.8518	235	867	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.8498	235	867	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.761	192	867	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.7401	237	867	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	77.7322	225	867	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	77.6291	220	867	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:59:14,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32019/tc_result.tsv
[2023-03-18 09:59:14,440] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:59:14,441] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:59:14,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdfbd02c-eaaf-46e7-96ce-77b1536e01aa/dqc_reference/checkm_data
[2023-03-18 09:59:14,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:59:14,446] [INFO] Task started: CheckM
[2023-03-18 09:59:14,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32019/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32019/checkm_input OceanDNA-b32019/checkm_result
[2023-03-18 09:59:57,295] [INFO] Task succeeded: CheckM
[2023-03-18 09:59:57,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:59:57,298] [INFO] ===== Completeness check finished =====
[2023-03-18 09:59:57,298] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:59:57,298] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32019/markers.fasta)
[2023-03-18 09:59:57,299] [INFO] Task started: Blastn
[2023-03-18 09:59:57,300] [INFO] Running command: blastn -query OceanDNA-b32019/markers.fasta -db /var/lib/cwl/stgcdfbd02c-eaaf-46e7-96ce-77b1536e01aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32019/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:58,735] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:58,736] [INFO] Selected 28 target genomes.
[2023-03-18 09:59:58,736] [INFO] Target genome list was writen to OceanDNA-b32019/target_genomes_gtdb.txt
[2023-03-18 09:59:58,837] [INFO] Task started: fastANI
[2023-03-18 09:59:58,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgd35a4e38-a5aa-407c-a381-dd72ab2c78f9/OceanDNA-b32019.fa --refList OceanDNA-b32019/target_genomes_gtdb.txt --output OceanDNA-b32019/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:00:14,566] [INFO] Task succeeded: fastANI
[2023-03-18 10:00:14,581] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:00:14,581] [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_001305965.1	s__Caenibius sp001305965	79.085	348	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.9672	336	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_009827405.1	s__Alteraurantiacibacter aestuarii	78.7806	202	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	78.7325	276	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCA_017302615.1	s__Novosphingobium sp017302615	78.6469	297	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860345.1	s__Caenibius tardaugens	78.639	327	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.6208	312	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016461955.1	s__QFOP01 sp003248785	78.5774	261	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__QFOP01	95.0	98.23	98.19	0.91	0.89	3	-
GCF_014652555.1	s__Novosphingobium colocasiae	78.413	312	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198665.1	s__Novosphingobium sp002198665	78.2952	287	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155425.1	s__Erythrobacter donghaensis	78.1913	245	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003454795.1	s__Novosphingobium sp003454795	78.1685	236	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_002813245.1	s__Novosphingobium kunmingense	78.1553	273	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660445.1	s__Croceibacterium ferulae	78.1215	255	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.1211	276	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002440635.1	s__Novosphingobium sp002440635	78.1072	258	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.1066	283	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	78.1039	231	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269345.1	s__Tsuneonella mangrovi	78.0375	226	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	78.0257	226	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958635.1	s__Altericroceibacterium_A xinjiangense	77.8937	224	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828055.1	s__Erythrobacter ramosus	77.8915	223	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903832325.1	s__Novosphingobium sp903832325	77.8622	281	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.98	99.94	0.97	0.96	4	-
GCF_014644315.1	s__Tsuneonella deserti	77.8477	184	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	77.8353	236	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141325.1	s__Novosphingobium sp013141325	77.7864	226	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827495.1	s__Tsuneonella aeria	77.726	232	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885425.1	s__Novosphingobium sp009885425	76.98	139	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:00:14,581] [INFO] GTDB search result was written to OceanDNA-b32019/result_gtdb.tsv
[2023-03-18 10:00:14,582] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:00:14,584] [INFO] DFAST_QC result json was written to OceanDNA-b32019/dqc_result.json
[2023-03-18 10:00:14,585] [INFO] DFAST_QC completed!
[2023-03-18 10:00:14,585] [INFO] Total running time: 0h1m38s