[2024-01-24 11:43:25,078] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg57a7ca4f-b381-4635-a62d-7db549e76006/dqc_reference
[2024-01-24 11:43:30,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,058] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,058] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3c9c9a3-3551-443c-ab69-f6dfaaf2b238/GCF_014196055.1_ASM1419605v1_genomic.fna.gz | prodigal -d GCF_014196055.1_ASM1419605v1_genomic.fna/cds.fna -a GCF_014196055.1_ASM1419605v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:43,639] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:43,639] [INFO] Task started: HMMsearch
[2024-01-24 11:43:43,640] [INFO] Running command: hmmsearch --tblout GCF_014196055.1_ASM1419605v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57a7ca4f-b381-4635-a62d-7db549e76006/dqc_reference/reference_markers.hmm GCF_014196055.1_ASM1419605v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:43,926] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:43,927] [INFO] Found 6/6 markers.
[2024-01-24 11:43:43,965] [INFO] Query marker FASTA was written to GCF_014196055.1_ASM1419605v1_genomic.fna/markers.fasta
[2024-01-24 11:43:43,965] [INFO] Task started: Blastn
[2024-01-24 11:43:43,965] [INFO] Running command: blastn -query GCF_014196055.1_ASM1419605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a7ca4f-b381-4635-a62d-7db549e76006/dqc_reference/reference_markers.fasta -out GCF_014196055.1_ASM1419605v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:44,872] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:44,876] [INFO] Selected 13 target genomes.
[2024-01-24 11:43:44,876] [INFO] Target genome list was writen to GCF_014196055.1_ASM1419605v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:44,881] [INFO] Task started: fastANI
[2024-01-24 11:43:44,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3c9c9a3-3551-443c-ab69-f6dfaaf2b238/GCF_014196055.1_ASM1419605v1_genomic.fna.gz --refList GCF_014196055.1_ASM1419605v1_genomic.fna/target_genomes.txt --output GCF_014196055.1_ASM1419605v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:56,539] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:56,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57a7ca4f-b381-4635-a62d-7db549e76006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:56,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57a7ca4f-b381-4635-a62d-7db549e76006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:56,551] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:56,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:56,551] [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 hassiacum	strain=DSM 14552	GCA_014196055.1	173676	173676	type	True	100.0	1438	1444	95	conclusive
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	81.9728	746	1444	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	81.7497	729	1444	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	81.7059	739	1444	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	81.4993	725	1444	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	81.447	711	1444	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	81.4364	722	1444	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	81.0472	608	1444	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	80.7166	591	1444	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	80.2249	584	1444	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.4854	373	1444	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.3765	385	1444	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.7942	256	1444	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:56,553] [INFO] DFAST Taxonomy check result was written to GCF_014196055.1_ASM1419605v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:56,554] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:56,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:56,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57a7ca4f-b381-4635-a62d-7db549e76006/dqc_reference/checkm_data
[2024-01-24 11:43:56,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:56,600] [INFO] Task started: CheckM
[2024-01-24 11:43:56,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196055.1_ASM1419605v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196055.1_ASM1419605v1_genomic.fna/checkm_input GCF_014196055.1_ASM1419605v1_genomic.fna/checkm_result
[2024-01-24 11:44:38,380] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:38,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:38,400] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:38,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:38,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196055.1_ASM1419605v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:38,401] [INFO] Task started: Blastn
[2024-01-24 11:44:38,401] [INFO] Running command: blastn -query GCF_014196055.1_ASM1419605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a7ca4f-b381-4635-a62d-7db549e76006/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196055.1_ASM1419605v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:40,128] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:40,131] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:40,132] [INFO] Target genome list was writen to GCF_014196055.1_ASM1419605v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:40,196] [INFO] Task started: fastANI
[2024-01-24 11:44:40,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3c9c9a3-3551-443c-ab69-f6dfaaf2b238/GCF_014196055.1_ASM1419605v1_genomic.fna.gz --refList GCF_014196055.1_ASM1419605v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196055.1_ASM1419605v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:51,973] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:51,988] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:51,988] [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_014196055.1	s__Novosphingobium hassiacum	100.0	1438	1444	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_015694345.1	s__Novosphingobium jiangmenense	81.9797	745	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830315.1	s__Novosphingobium taihuense	81.7425	731	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003454795.1	s__Novosphingobium sp003454795	81.6655	727	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	81.4759	726	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000807925.1	s__Novosphingobium subterraneum	81.4531	721	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCF_900176395.1	s__Novosphingobium sp900176395	81.4081	702	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641335.1	s__Novosphingobium sp012641335	81.1987	717	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256985.1	s__Novosphingobium sp002256985	81.1082	665	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.95	99.92	0.97	0.95	3	-
GCA_002256775.1	s__Novosphingobium sp002256775	81.0956	596	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280675.1	s__Novosphingobium sp002280675	80.686	604	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117425.1	s__Novosphingobium sp900117425	79.9126	558	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.26	96.76	0.88	0.87	3	-
GCF_004364785.1	s__Novosphingobium sp004364785	79.8705	568	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:51,990] [INFO] GTDB search result was written to GCF_014196055.1_ASM1419605v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:51,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:51,994] [INFO] DFAST_QC result json was written to GCF_014196055.1_ASM1419605v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:51,994] [INFO] DFAST_QC completed!
[2024-01-24 11:44:51,994] [INFO] Total running time: 0h1m27s