[2024-01-24 12:23:35,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,993] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg98c692d7-d514-41b5-8abd-8146d577a6fb/dqc_reference
[2024-01-24 12:23:37,330] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:37,330] [INFO] Task started: Prodigal
[2024-01-24 12:23:37,331] [INFO] Running command: gunzip -c /var/lib/cwl/stgec897542-f1b4-40f9-be2d-eee95330c002/GCF_028607105.1_ASM2860710v1_genomic.fna.gz | prodigal -d GCF_028607105.1_ASM2860710v1_genomic.fna/cds.fna -a GCF_028607105.1_ASM2860710v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:53,622] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:53,622] [INFO] Task started: HMMsearch
[2024-01-24 12:23:53,623] [INFO] Running command: hmmsearch --tblout GCF_028607105.1_ASM2860710v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98c692d7-d514-41b5-8abd-8146d577a6fb/dqc_reference/reference_markers.hmm GCF_028607105.1_ASM2860710v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:53,925] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:53,927] [INFO] Found 6/6 markers.
[2024-01-24 12:23:53,973] [INFO] Query marker FASTA was written to GCF_028607105.1_ASM2860710v1_genomic.fna/markers.fasta
[2024-01-24 12:23:53,974] [INFO] Task started: Blastn
[2024-01-24 12:23:53,974] [INFO] Running command: blastn -query GCF_028607105.1_ASM2860710v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98c692d7-d514-41b5-8abd-8146d577a6fb/dqc_reference/reference_markers.fasta -out GCF_028607105.1_ASM2860710v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:54,919] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:54,924] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:54,924] [INFO] Target genome list was writen to GCF_028607105.1_ASM2860710v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:54,929] [INFO] Task started: fastANI
[2024-01-24 12:23:54,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgec897542-f1b4-40f9-be2d-eee95330c002/GCF_028607105.1_ASM2860710v1_genomic.fna.gz --refList GCF_028607105.1_ASM2860710v1_genomic.fna/target_genomes.txt --output GCF_028607105.1_ASM2860710v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:07,331] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:07,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98c692d7-d514-41b5-8abd-8146d577a6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:07,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98c692d7-d514-41b5-8abd-8146d577a6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:07,358] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:07,358] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:07,358] [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 sediminicola	strain=DSM 27057	GCA_014196525.1	563162	563162	type	True	90.9674	1299	1628	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	82.0945	815	1628	95	below_threshold
Novosphingobium ovatum	strain=FSY-8	GCA_009909235.1	1908523	1908523	type	True	81.3919	724	1628	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	79.9833	733	1628	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.8916	423	1628	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.6715	466	1628	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.5497	354	1628	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.5441	389	1628	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	78.5361	404	1628	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	78.433	411	1628	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	78.3267	413	1628	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	78.1327	388	1628	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	78.1302	331	1628	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.8787	287	1628	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.5341	224	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:07,360] [INFO] DFAST Taxonomy check result was written to GCF_028607105.1_ASM2860710v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:07,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:07,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:07,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98c692d7-d514-41b5-8abd-8146d577a6fb/dqc_reference/checkm_data
[2024-01-24 12:24:07,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:07,409] [INFO] Task started: CheckM
[2024-01-24 12:24:07,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028607105.1_ASM2860710v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028607105.1_ASM2860710v1_genomic.fna/checkm_input GCF_028607105.1_ASM2860710v1_genomic.fna/checkm_result
[2024-01-24 12:25:02,636] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:02,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:02,660] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:02,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:02,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028607105.1_ASM2860710v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:02,661] [INFO] Task started: Blastn
[2024-01-24 12:25:02,661] [INFO] Running command: blastn -query GCF_028607105.1_ASM2860710v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98c692d7-d514-41b5-8abd-8146d577a6fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_028607105.1_ASM2860710v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:04,368] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:04,373] [INFO] Selected 7 target genomes.
[2024-01-24 12:25:04,373] [INFO] Target genome list was writen to GCF_028607105.1_ASM2860710v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:04,404] [INFO] Task started: fastANI
[2024-01-24 12:25:04,404] [INFO] Running command: fastANI --query /var/lib/cwl/stgec897542-f1b4-40f9-be2d-eee95330c002/GCF_028607105.1_ASM2860710v1_genomic.fna.gz --refList GCF_028607105.1_ASM2860710v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028607105.1_ASM2860710v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:13,290] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:13,300] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:25:13,300] [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_012275515.1	s__Novosphingobium sp001898925	93.0969	1374	1628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.48	97.63	0.91	0.85	4	-
GCF_014196525.1	s__Novosphingobium sediminicola	90.996	1296	1628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149295.1	s__Novosphingobium sp013149295	90.8928	1314	1628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005905.1	s__Novosphingobium umbonatum	82.0604	817	1628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336765.1	s__Novosphingobium sp002336765	81.4465	499	1628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909235.1	s__Novosphingobium sp009909235	81.3721	726	1628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017163935.1	s__Novosphingobium sp017163935	80.1054	730	1628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:13,302] [INFO] GTDB search result was written to GCF_028607105.1_ASM2860710v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:13,302] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:13,305] [INFO] DFAST_QC result json was written to GCF_028607105.1_ASM2860710v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:13,306] [INFO] DFAST_QC completed!
[2024-01-24 12:25:13,306] [INFO] Total running time: 0h1m37s