[2024-01-24 13:13:03,124] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:03,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:03,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg071fc593-1f33-4f73-a9b9-2d4c44ed57f6/dqc_reference
[2024-01-24 13:13:04,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:04,336] [INFO] Task started: Prodigal
[2024-01-24 13:13:04,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg08b9231f-062b-4403-abf7-f54b0b8297e4/GCF_014196525.1_ASM1419652v1_genomic.fna.gz | prodigal -d GCF_014196525.1_ASM1419652v1_genomic.fna/cds.fna -a GCF_014196525.1_ASM1419652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:21,869] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:21,869] [INFO] Task started: HMMsearch
[2024-01-24 13:13:21,870] [INFO] Running command: hmmsearch --tblout GCF_014196525.1_ASM1419652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg071fc593-1f33-4f73-a9b9-2d4c44ed57f6/dqc_reference/reference_markers.hmm GCF_014196525.1_ASM1419652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:22,152] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:22,154] [INFO] Found 6/6 markers.
[2024-01-24 13:13:22,198] [INFO] Query marker FASTA was written to GCF_014196525.1_ASM1419652v1_genomic.fna/markers.fasta
[2024-01-24 13:13:22,199] [INFO] Task started: Blastn
[2024-01-24 13:13:22,199] [INFO] Running command: blastn -query GCF_014196525.1_ASM1419652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg071fc593-1f33-4f73-a9b9-2d4c44ed57f6/dqc_reference/reference_markers.fasta -out GCF_014196525.1_ASM1419652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:23,122] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:23,126] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:23,127] [INFO] Target genome list was writen to GCF_014196525.1_ASM1419652v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:23,163] [INFO] Task started: fastANI
[2024-01-24 13:13:23,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b9231f-062b-4403-abf7-f54b0b8297e4/GCF_014196525.1_ASM1419652v1_genomic.fna.gz --refList GCF_014196525.1_ASM1419652v1_genomic.fna/target_genomes.txt --output GCF_014196525.1_ASM1419652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:35,604] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:35,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg071fc593-1f33-4f73-a9b9-2d4c44ed57f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:35,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg071fc593-1f33-4f73-a9b9-2d4c44ed57f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:35,624] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:35,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:35,624] [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	100.0	1760	1765	95	conclusive
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	81.9024	875	1765	95	below_threshold
Novosphingobium ovatum	strain=FSY-8	GCA_009909235.1	1908523	1908523	type	True	81.1531	738	1765	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	79.9455	815	1765	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.6571	450	1765	95	below_threshold
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	78.505	523	1765	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.4681	436	1765	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.4295	375	1765	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.1481	403	1765	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	78.1399	379	1765	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.8948	342	1765	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	77.7371	392	1765	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.5375	213	1765	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.5341	233	1765	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.5254	277	1765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:35,626] [INFO] DFAST Taxonomy check result was written to GCF_014196525.1_ASM1419652v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:35,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:35,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:35,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg071fc593-1f33-4f73-a9b9-2d4c44ed57f6/dqc_reference/checkm_data
[2024-01-24 13:13:35,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:35,679] [INFO] Task started: CheckM
[2024-01-24 13:13:35,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196525.1_ASM1419652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196525.1_ASM1419652v1_genomic.fna/checkm_input GCF_014196525.1_ASM1419652v1_genomic.fna/checkm_result
[2024-01-24 13:14:28,230] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:28,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:28,254] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:28,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:28,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196525.1_ASM1419652v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:28,255] [INFO] Task started: Blastn
[2024-01-24 13:14:28,255] [INFO] Running command: blastn -query GCF_014196525.1_ASM1419652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg071fc593-1f33-4f73-a9b9-2d4c44ed57f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196525.1_ASM1419652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:30,213] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:30,215] [INFO] Selected 7 target genomes.
[2024-01-24 13:14:30,216] [INFO] Target genome list was writen to GCF_014196525.1_ASM1419652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:30,243] [INFO] Task started: fastANI
[2024-01-24 13:14:30,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b9231f-062b-4403-abf7-f54b0b8297e4/GCF_014196525.1_ASM1419652v1_genomic.fna.gz --refList GCF_014196525.1_ASM1419652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196525.1_ASM1419652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:38,776] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:38,790] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:38,790] [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_014196525.1	s__Novosphingobium sediminicola	100.0	1760	1765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013149295.1	s__Novosphingobium sp013149295	93.5761	1547	1765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275515.1	s__Novosphingobium sp001898925	92.2081	1433	1765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.48	97.63	0.91	0.85	4	-
GCF_004005905.1	s__Novosphingobium umbonatum	81.9175	873	1765	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	81.4105	492	1765	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	81.1256	743	1765	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	79.8472	776	1765	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 13:14:38,793] [INFO] GTDB search result was written to GCF_014196525.1_ASM1419652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:38,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:38,799] [INFO] DFAST_QC result json was written to GCF_014196525.1_ASM1419652v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:38,799] [INFO] DFAST_QC completed!
[2024-01-24 13:14:38,799] [INFO] Total running time: 0h1m36s