[2023-06-28 21:58:15,655] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:58:15,664] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:58:15,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg597bcd12-5f47-4f97-af37-c97fc1976646/dqc_reference
[2023-06-28 21:58:16,911] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:58:16,917] [INFO] Task started: Prodigal
[2023-06-28 21:58:16,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg605b1c85-0641-46f8-96f3-988d415531e1/GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna.gz | prodigal -d GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/cds.fna -a GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:58:24,746] [INFO] Task succeeded: Prodigal
[2023-06-28 21:58:24,747] [INFO] Task started: HMMsearch
[2023-06-28 21:58:24,747] [INFO] Running command: hmmsearch --tblout GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg597bcd12-5f47-4f97-af37-c97fc1976646/dqc_reference/reference_markers.hmm GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:58:24,993] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:58:24,994] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg605b1c85-0641-46f8-96f3-988d415531e1/GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna.gz]
[2023-06-28 21:58:25,032] [INFO] Query marker FASTA was written to GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/markers.fasta
[2023-06-28 21:58:25,032] [INFO] Task started: Blastn
[2023-06-28 21:58:25,032] [INFO] Running command: blastn -query GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/markers.fasta -db /var/lib/cwl/stg597bcd12-5f47-4f97-af37-c97fc1976646/dqc_reference/reference_markers.fasta -out GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:58:25,845] [INFO] Task succeeded: Blastn
[2023-06-28 21:58:25,849] [INFO] Selected 20 target genomes.
[2023-06-28 21:58:25,850] [INFO] Target genome list was writen to GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/target_genomes.txt
[2023-06-28 21:58:25,884] [INFO] Task started: fastANI
[2023-06-28 21:58:25,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg605b1c85-0641-46f8-96f3-988d415531e1/GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna.gz --refList GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/target_genomes.txt --output GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:58:40,515] [INFO] Task succeeded: fastANI
[2023-06-28 21:58:40,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg597bcd12-5f47-4f97-af37-c97fc1976646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:58:40,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg597bcd12-5f47-4f97-af37-c97fc1976646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:58:40,532] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 21:58:40,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 21:58:40,533] [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 fluoreni	strain=DSM 27568	GCA_014196615.1	1391222	1391222	type	True	97.0214	426	742	95	conclusive
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	79.2411	193	742	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.1375	197	742	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	79.0925	221	742	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	79.0629	178	742	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	79.0003	183	742	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	78.922	214	742	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.8878	197	742	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	78.8872	173	742	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	78.828	184	742	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.8151	175	742	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.6937	165	742	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.6586	174	742	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.6554	181	742	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	78.6518	182	742	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	78.4078	178	742	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.2986	169	742	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.5944	131	742	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	76.9998	109	742	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	76.9601	114	742	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:58:40,535] [INFO] DFAST Taxonomy check result was written to GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/tc_result.tsv
[2023-06-28 21:58:40,536] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:58:40,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:58:40,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg597bcd12-5f47-4f97-af37-c97fc1976646/dqc_reference/checkm_data
[2023-06-28 21:58:40,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:58:40,585] [INFO] Task started: CheckM
[2023-06-28 21:58:40,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/checkm_input GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/checkm_result
[2023-06-28 21:59:08,512] [INFO] Task succeeded: CheckM
[2023-06-28 21:59:08,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 21:59:08,538] [INFO] ===== Completeness check finished =====
[2023-06-28 21:59:08,538] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:59:08,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/markers.fasta)
[2023-06-28 21:59:08,539] [INFO] Task started: Blastn
[2023-06-28 21:59:08,539] [INFO] Running command: blastn -query GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/markers.fasta -db /var/lib/cwl/stg597bcd12-5f47-4f97-af37-c97fc1976646/dqc_reference/reference_markers_gtdb.fasta -out GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:59:09,830] [INFO] Task succeeded: Blastn
[2023-06-28 21:59:09,835] [INFO] Selected 14 target genomes.
[2023-06-28 21:59:09,835] [INFO] Target genome list was writen to GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:59:09,848] [INFO] Task started: fastANI
[2023-06-28 21:59:09,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg605b1c85-0641-46f8-96f3-988d415531e1/GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna.gz --refList GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/target_genomes_gtdb.txt --output GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:59:20,520] [INFO] Task succeeded: fastANI
[2023-06-28 21:59:20,540] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:59:20,540] [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_014196615.1	s__Novosphingobium fluoreni	97.0224	426	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.16	97.16	0.90	0.90	2	conclusive
GCF_902506425.1	s__Novosphingobium sp902506425	81.4392	277	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204535.1	s__Novosphingobium chloroacetimidivorans	81.4036	286	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272475.1	s__Novosphingobium sp000272475	79.2692	206	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281975.1	s__Novosphingobium sp000281975	79.2424	209	742	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	79.1837	216	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_001742225.1	s__Novosphingobium resinovorum	79.1208	232	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_001046635.1	s__Novosphingobium barchaimii	79.073	222	742	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	78.95	195	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645195.1	s__Novosphingobium indicum	78.8622	174	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCA_004211435.1	s__Novosphingobium sp004211435	78.7774	168	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019075875.1	s__Novosphingobium sp019075875	78.2934	194	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	77.6149	130	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641655.1	s__Alteriqipengyuania_A marina	77.5993	99	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-28 21:59:20,542] [INFO] GTDB search result was written to GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/result_gtdb.tsv
[2023-06-28 21:59:20,542] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:59:20,546] [INFO] DFAST_QC result json was written to GCA_913778485.1_SP287_3_metabat2_genome_mining.19_cleaned_genomic.fna/dqc_result.json
[2023-06-28 21:59:20,547] [INFO] DFAST_QC completed!
[2023-06-28 21:59:20,547] [INFO] Total running time: 0h1m5s