[2024-01-24 15:19:04,418] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,420] [INFO] DQC Reference Directory: /var/lib/cwl/stga096592b-2090-47ca-bb52-e24beada11b1/dqc_reference
[2024-01-24 15:19:05,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,661] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,662] [INFO] Running command: gunzip -c /var/lib/cwl/stg92666dc3-2b08-4ae4-8461-b3b93f68d35f/GCF_007954425.1_ASM795442v1_genomic.fna.gz | prodigal -d GCF_007954425.1_ASM795442v1_genomic.fna/cds.fna -a GCF_007954425.1_ASM795442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:15,089] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:15,089] [INFO] Task started: HMMsearch
[2024-01-24 15:19:15,090] [INFO] Running command: hmmsearch --tblout GCF_007954425.1_ASM795442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga096592b-2090-47ca-bb52-e24beada11b1/dqc_reference/reference_markers.hmm GCF_007954425.1_ASM795442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:15,350] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:15,351] [INFO] Found 6/6 markers.
[2024-01-24 15:19:15,386] [INFO] Query marker FASTA was written to GCF_007954425.1_ASM795442v1_genomic.fna/markers.fasta
[2024-01-24 15:19:15,386] [INFO] Task started: Blastn
[2024-01-24 15:19:15,387] [INFO] Running command: blastn -query GCF_007954425.1_ASM795442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga096592b-2090-47ca-bb52-e24beada11b1/dqc_reference/reference_markers.fasta -out GCF_007954425.1_ASM795442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:16,297] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:16,309] [INFO] Selected 20 target genomes.
[2024-01-24 15:19:16,309] [INFO] Target genome list was writen to GCF_007954425.1_ASM795442v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:16,340] [INFO] Task started: fastANI
[2024-01-24 15:19:16,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg92666dc3-2b08-4ae4-8461-b3b93f68d35f/GCF_007954425.1_ASM795442v1_genomic.fna.gz --refList GCF_007954425.1_ASM795442v1_genomic.fna/target_genomes.txt --output GCF_007954425.1_ASM795442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:30,615] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:30,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga096592b-2090-47ca-bb52-e24beada11b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:30,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga096592b-2090-47ca-bb52-e24beada11b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:30,631] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:30,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:30,631] [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 ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	100.0	1037	1039	95	conclusive
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	80.7879	584	1039	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	80.3729	533	1039	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	79.9872	457	1039	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	79.6773	440	1039	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.507	442	1039	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	79.3214	452	1039	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	79.0376	388	1039	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	79.006	396	1039	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	79.0058	377	1039	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	78.8891	438	1039	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.7148	311	1039	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	78.5207	277	1039	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.5075	279	1039	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.5031	375	1039	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.4702	371	1039	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.3685	331	1039	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.2492	305	1039	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.1307	288	1039	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.0427	311	1039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:30,633] [INFO] DFAST Taxonomy check result was written to GCF_007954425.1_ASM795442v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:30,634] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:30,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:30,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga096592b-2090-47ca-bb52-e24beada11b1/dqc_reference/checkm_data
[2024-01-24 15:19:30,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:30,689] [INFO] Task started: CheckM
[2024-01-24 15:19:30,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007954425.1_ASM795442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007954425.1_ASM795442v1_genomic.fna/checkm_input GCF_007954425.1_ASM795442v1_genomic.fna/checkm_result
[2024-01-24 15:20:02,039] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:02,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:02,061] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:02,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:02,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007954425.1_ASM795442v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:02,063] [INFO] Task started: Blastn
[2024-01-24 15:20:02,063] [INFO] Running command: blastn -query GCF_007954425.1_ASM795442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga096592b-2090-47ca-bb52-e24beada11b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_007954425.1_ASM795442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:03,709] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:03,713] [INFO] Selected 10 target genomes.
[2024-01-24 15:20:03,713] [INFO] Target genome list was writen to GCF_007954425.1_ASM795442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:03,723] [INFO] Task started: fastANI
[2024-01-24 15:20:03,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg92666dc3-2b08-4ae4-8461-b3b93f68d35f/GCF_007954425.1_ASM795442v1_genomic.fna.gz --refList GCF_007954425.1_ASM795442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007954425.1_ASM795442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:11,603] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:11,616] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:11,616] [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_007954425.1	s__Novosphingobium ginsenosidimutans	100.0	1037	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002454125.1	s__Novosphingobium sp002454125	90.0038	655	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657645.1	s__Novosphingobium sp015657645	87.0359	687	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926135.1	s__Novosphingobium sp009926135	85.6193	770	1039	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	81.7788	594	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719755.1	s__Novosphingobium sp016719755	80.9859	574	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCA_002440635.1	s__Novosphingobium sp002440635	80.8687	580	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652615.1	s__Novosphingobium arvoryzae	80.7775	585	1039	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	80.3732	533	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241045.1	s__Novosphingobium sp018241045	80.2287	380	1039	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 15:20:11,617] [INFO] GTDB search result was written to GCF_007954425.1_ASM795442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:11,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:11,622] [INFO] DFAST_QC result json was written to GCF_007954425.1_ASM795442v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:11,622] [INFO] DFAST_QC completed!
[2024-01-24 15:20:11,622] [INFO] Total running time: 0h1m7s