[2024-01-24 12:44:43,846] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,850] [INFO] DQC Reference Directory: /var/lib/cwl/stgba75a2b2-1fa9-4c1d-befb-954cb703a33e/dqc_reference
[2024-01-24 12:44:45,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,247] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg7377ee9c-2270-4eae-a6e7-789d76ae5a73/GCF_018417475.1_ASM1841747v1_genomic.fna.gz | prodigal -d GCF_018417475.1_ASM1841747v1_genomic.fna/cds.fna -a GCF_018417475.1_ASM1841747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:00,339] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:00,339] [INFO] Task started: HMMsearch
[2024-01-24 12:45:00,339] [INFO] Running command: hmmsearch --tblout GCF_018417475.1_ASM1841747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba75a2b2-1fa9-4c1d-befb-954cb703a33e/dqc_reference/reference_markers.hmm GCF_018417475.1_ASM1841747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:00,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:00,683] [INFO] Found 6/6 markers.
[2024-01-24 12:45:00,722] [INFO] Query marker FASTA was written to GCF_018417475.1_ASM1841747v1_genomic.fna/markers.fasta
[2024-01-24 12:45:00,722] [INFO] Task started: Blastn
[2024-01-24 12:45:00,722] [INFO] Running command: blastn -query GCF_018417475.1_ASM1841747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba75a2b2-1fa9-4c1d-befb-954cb703a33e/dqc_reference/reference_markers.fasta -out GCF_018417475.1_ASM1841747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:01,819] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:01,822] [INFO] Selected 13 target genomes.
[2024-01-24 12:45:01,823] [INFO] Target genome list was writen to GCF_018417475.1_ASM1841747v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:01,825] [INFO] Task started: fastANI
[2024-01-24 12:45:01,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg7377ee9c-2270-4eae-a6e7-789d76ae5a73/GCF_018417475.1_ASM1841747v1_genomic.fna.gz --refList GCF_018417475.1_ASM1841747v1_genomic.fna/target_genomes.txt --output GCF_018417475.1_ASM1841747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:16,265] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:16,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba75a2b2-1fa9-4c1d-befb-954cb703a33e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:16,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba75a2b2-1fa9-4c1d-befb-954cb703a33e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:16,278] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:16,278] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:16,279] [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 decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	100.0	1583	1583	95	conclusive
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	84.6244	994	1583	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	82.9666	879	1583	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	80.973	607	1583	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	80.9615	589	1583	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	80.9038	675	1583	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	80.8151	612	1583	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	80.8025	605	1583	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.7311	644	1583	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	80.3512	598	1583	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.9876	528	1583	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.3989	484	1583	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.99	487	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:16,280] [INFO] DFAST Taxonomy check result was written to GCF_018417475.1_ASM1841747v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:16,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:16,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:16,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba75a2b2-1fa9-4c1d-befb-954cb703a33e/dqc_reference/checkm_data
[2024-01-24 12:45:16,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:16,345] [INFO] Task started: CheckM
[2024-01-24 12:45:16,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018417475.1_ASM1841747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018417475.1_ASM1841747v1_genomic.fna/checkm_input GCF_018417475.1_ASM1841747v1_genomic.fna/checkm_result
[2024-01-24 12:46:02,682] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:02,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:02,711] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:02,712] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:02,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018417475.1_ASM1841747v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:02,713] [INFO] Task started: Blastn
[2024-01-24 12:46:02,713] [INFO] Running command: blastn -query GCF_018417475.1_ASM1841747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba75a2b2-1fa9-4c1d-befb-954cb703a33e/dqc_reference/reference_markers_gtdb.fasta -out GCF_018417475.1_ASM1841747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:04,518] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:04,522] [INFO] Selected 11 target genomes.
[2024-01-24 12:46:04,522] [INFO] Target genome list was writen to GCF_018417475.1_ASM1841747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:04,525] [INFO] Task started: fastANI
[2024-01-24 12:46:04,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg7377ee9c-2270-4eae-a6e7-789d76ae5a73/GCF_018417475.1_ASM1841747v1_genomic.fna.gz --refList GCF_018417475.1_ASM1841747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018417475.1_ASM1841747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:18,317] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:18,326] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:18,326] [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_018417475.1	s__Novosphingobium sp000813185	100.0	1583	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	conclusive
GCF_008107685.1	s__Novosphingobium sp008107685	91.7105	1159	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	84.6422	992	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015865035.1	s__Novosphingobium sp015865035	82.9571	880	1583	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	81.4685	739	1583	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	81.0156	725	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	80.9451	612	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	80.919	673	1583	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	80.693	648	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCF_000802225.1	s__Novosphingobium malaysiense	80.3601	597	1583	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	80.3004	603	1583	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 12:46:18,328] [INFO] GTDB search result was written to GCF_018417475.1_ASM1841747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:18,329] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:18,332] [INFO] DFAST_QC result json was written to GCF_018417475.1_ASM1841747v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:18,332] [INFO] DFAST_QC completed!
[2024-01-24 12:46:18,332] [INFO] Total running time: 0h1m34s