[2023-03-16 11:24:22,163] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:24:22,163] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:24:22,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3192a3a-7f3f-4b60-996f-40e7f20643fd/dqc_reference
[2023-03-16 11:24:24,008] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:24:24,009] [INFO] Task started: Prodigal
[2023-03-16 11:24:24,009] [INFO] Running command: cat /var/lib/cwl/stg24bafedd-4a54-4e88-850d-d26ab28302de/OceanDNA-b31981.fa | prodigal -d OceanDNA-b31981/cds.fna -a OceanDNA-b31981/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:24:53,251] [INFO] Task succeeded: Prodigal
[2023-03-16 11:24:53,251] [INFO] Task started: HMMsearch
[2023-03-16 11:24:53,251] [INFO] Running command: hmmsearch --tblout OceanDNA-b31981/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3192a3a-7f3f-4b60-996f-40e7f20643fd/dqc_reference/reference_markers.hmm OceanDNA-b31981/protein.faa > /dev/null
[2023-03-16 11:24:53,437] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:24:53,438] [INFO] Found 6/6 markers.
[2023-03-16 11:24:53,457] [INFO] Query marker FASTA was written to OceanDNA-b31981/markers.fasta
[2023-03-16 11:24:53,459] [INFO] Task started: Blastn
[2023-03-16 11:24:53,459] [INFO] Running command: blastn -query OceanDNA-b31981/markers.fasta -db /var/lib/cwl/stgd3192a3a-7f3f-4b60-996f-40e7f20643fd/dqc_reference/reference_markers.fasta -out OceanDNA-b31981/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:24:54,149] [INFO] Task succeeded: Blastn
[2023-03-16 11:24:54,149] [INFO] Selected 21 target genomes.
[2023-03-16 11:24:54,150] [INFO] Target genome list was writen to OceanDNA-b31981/target_genomes.txt
[2023-03-16 11:24:54,162] [INFO] Task started: fastANI
[2023-03-16 11:24:54,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg24bafedd-4a54-4e88-850d-d26ab28302de/OceanDNA-b31981.fa --refList OceanDNA-b31981/target_genomes.txt --output OceanDNA-b31981/fastani_result.tsv --threads 1
[2023-03-16 11:25:08,856] [INFO] Task succeeded: fastANI
[2023-03-16 11:25:08,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3192a3a-7f3f-4b60-996f-40e7f20643fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:25:08,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3192a3a-7f3f-4b60-996f-40e7f20643fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:25:08,868] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:25:08,868] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:25:08,868] [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
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	79.354	403	1027	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	78.9493	406	1027	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	78.8205	350	1027	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	78.4763	370	1027	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	78.4739	364	1027	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	78.4398	371	1027	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.3703	365	1027	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.2349	314	1027	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	78.2035	323	1027	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.1868	353	1027	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.1559	299	1027	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	78.1325	296	1027	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	78.125	276	1027	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	78.0632	291	1027	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.0272	333	1027	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.9014	262	1027	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	77.8129	271	1027	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	77.8108	315	1027	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	77.6523	232	1027	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	77.4467	262	1027	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.0873	197	1027	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:25:08,868] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31981/tc_result.tsv
[2023-03-16 11:25:08,868] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:25:08,868] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:25:08,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3192a3a-7f3f-4b60-996f-40e7f20643fd/dqc_reference/checkm_data
[2023-03-16 11:25:08,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:25:08,875] [INFO] Task started: CheckM
[2023-03-16 11:25:08,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31981/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31981/checkm_input OceanDNA-b31981/checkm_result
[2023-03-16 11:25:58,289] [INFO] Task succeeded: CheckM
[2023-03-16 11:25:58,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:25:58,292] [INFO] ===== Completeness check finished =====
[2023-03-16 11:25:58,292] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:25:58,292] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31981/markers.fasta)
[2023-03-16 11:25:58,294] [INFO] Task started: Blastn
[2023-03-16 11:25:58,294] [INFO] Running command: blastn -query OceanDNA-b31981/markers.fasta -db /var/lib/cwl/stgd3192a3a-7f3f-4b60-996f-40e7f20643fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31981/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:25:59,404] [INFO] Task succeeded: Blastn
[2023-03-16 11:25:59,405] [INFO] Selected 23 target genomes.
[2023-03-16 11:25:59,405] [INFO] Target genome list was writen to OceanDNA-b31981/target_genomes_gtdb.txt
[2023-03-16 11:25:59,899] [INFO] Task started: fastANI
[2023-03-16 11:25:59,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg24bafedd-4a54-4e88-850d-d26ab28302de/OceanDNA-b31981.fa --refList OceanDNA-b31981/target_genomes_gtdb.txt --output OceanDNA-b31981/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:26:16,380] [INFO] Task succeeded: fastANI
[2023-03-16 11:26:16,394] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:26:16,395] [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_014645195.1	s__Novosphingobium indicum	79.3425	404	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	78.9233	409	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	78.8326	414	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802225.1	s__Novosphingobium malaysiense	78.8271	350	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113255.1	s__Novosphingobium sp900113255	78.7216	385	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	78.5939	309	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145025.1	s__Novosphingobium sp005145025	78.533	350	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014975.1	s__Novosphingobium sp002336885	78.4885	343	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	78.4763	370	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCA_001725355.1	s__Novosphingobium sp001725355	78.4025	321	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874585.1	s__Novosphingobium sp006874585	78.3046	360	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	78.2606	339	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408095.1	s__Novosphingobium marinum	78.1933	324	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014652615.1	s__Novosphingobium arvoryzae	78.1864	353	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813245.1	s__Novosphingobium kunmingense	78.1474	301	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	78.1345	318	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694345.1	s__Novosphingobium jiangmenense	78.1289	275	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230355.1	s__Novosphingobium piscinae	78.1101	298	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421325.1	s__Novosphingobium sp001421325	78.1074	291	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015865035.1	s__Novosphingobium sp015865035	77.832	313	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970225.1	s__Novosphingobium sp903970225	77.5542	228	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971065.1	s__Novosphingobium sp018971065	77.5487	281	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903923465.1	s__Novosphingobium sp903923465	77.4754	224	1027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:26:16,395] [INFO] GTDB search result was written to OceanDNA-b31981/result_gtdb.tsv
[2023-03-16 11:26:16,395] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:26:16,397] [INFO] DFAST_QC result json was written to OceanDNA-b31981/dqc_result.json
[2023-03-16 11:26:16,397] [INFO] DFAST_QC completed!
[2023-03-16 11:26:16,397] [INFO] Total running time: 0h1m54s