[2024-01-24 15:26:39,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f58c055-1863-4ed7-8b26-cbe6e89f4732/dqc_reference
[2024-01-24 15:26:41,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,208] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,208] [INFO] Running command: gunzip -c /var/lib/cwl/stgd14ef1f1-0589-4252-adad-2882c87e44d6/GCF_014196615.1_ASM1419661v1_genomic.fna.gz | prodigal -d GCF_014196615.1_ASM1419661v1_genomic.fna/cds.fna -a GCF_014196615.1_ASM1419661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:52,501] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:52,501] [INFO] Task started: HMMsearch
[2024-01-24 15:26:52,501] [INFO] Running command: hmmsearch --tblout GCF_014196615.1_ASM1419661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f58c055-1863-4ed7-8b26-cbe6e89f4732/dqc_reference/reference_markers.hmm GCF_014196615.1_ASM1419661v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:52,797] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:52,799] [INFO] Found 6/6 markers.
[2024-01-24 15:26:52,836] [INFO] Query marker FASTA was written to GCF_014196615.1_ASM1419661v1_genomic.fna/markers.fasta
[2024-01-24 15:26:52,836] [INFO] Task started: Blastn
[2024-01-24 15:26:52,837] [INFO] Running command: blastn -query GCF_014196615.1_ASM1419661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f58c055-1863-4ed7-8b26-cbe6e89f4732/dqc_reference/reference_markers.fasta -out GCF_014196615.1_ASM1419661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:53,767] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:53,771] [INFO] Selected 22 target genomes.
[2024-01-24 15:26:53,771] [INFO] Target genome list was writen to GCF_014196615.1_ASM1419661v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:53,791] [INFO] Task started: fastANI
[2024-01-24 15:26:53,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgd14ef1f1-0589-4252-adad-2882c87e44d6/GCF_014196615.1_ASM1419661v1_genomic.fna.gz --refList GCF_014196615.1_ASM1419661v1_genomic.fna/target_genomes.txt --output GCF_014196615.1_ASM1419661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:12,849] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:12,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f58c055-1863-4ed7-8b26-cbe6e89f4732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:12,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f58c055-1863-4ed7-8b26-cbe6e89f4732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:12,868] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:12,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:12,869] [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 fluoreni	strain=DSM 27568	GCA_014196615.1	1391222	1391222	type	True	100.0	1188	1189	95	conclusive
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	79.4995	465	1189	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	79.3897	442	1189	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.325	451	1189	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	79.3244	426	1189	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	79.2659	387	1189	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	79.2041	419	1189	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	79.1928	467	1189	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	79.1902	427	1189	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	79.1648	491	1189	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	79.1086	430	1189	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	79.0959	421	1189	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	79.0821	347	1189	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.8693	370	1189	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	78.8573	408	1189	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.8319	443	1189	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	78.7425	415	1189	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.6914	385	1189	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.6857	392	1189	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	78.644	380	1189	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.9745	285	1189	95	below_threshold
Croceicoccus mobilis	strain=CGMCC 1.15360	GCA_014642595.1	1703339	1703339	type	True	77.798	254	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:12,871] [INFO] DFAST Taxonomy check result was written to GCF_014196615.1_ASM1419661v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:12,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:12,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:12,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f58c055-1863-4ed7-8b26-cbe6e89f4732/dqc_reference/checkm_data
[2024-01-24 15:27:12,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:12,909] [INFO] Task started: CheckM
[2024-01-24 15:27:12,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196615.1_ASM1419661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196615.1_ASM1419661v1_genomic.fna/checkm_input GCF_014196615.1_ASM1419661v1_genomic.fna/checkm_result
[2024-01-24 15:27:48,723] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:48,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:48,742] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:48,743] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:48,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196615.1_ASM1419661v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:48,743] [INFO] Task started: Blastn
[2024-01-24 15:27:48,744] [INFO] Running command: blastn -query GCF_014196615.1_ASM1419661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f58c055-1863-4ed7-8b26-cbe6e89f4732/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196615.1_ASM1419661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:50,315] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:50,319] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:50,319] [INFO] Target genome list was writen to GCF_014196615.1_ASM1419661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:50,331] [INFO] Task started: fastANI
[2024-01-24 15:27:50,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgd14ef1f1-0589-4252-adad-2882c87e44d6/GCF_014196615.1_ASM1419661v1_genomic.fna.gz --refList GCF_014196615.1_ASM1419661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196615.1_ASM1419661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:05,386] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:05,399] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:05,399] [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_014196615.1	s__Novosphingobium fluoreni	100.0	1188	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.16	97.16	0.90	0.90	2	conclusive
GCF_014204535.1	s__Novosphingobium chloroacetimidivorans	81.9046	642	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506425.1	s__Novosphingobium sp902506425	81.7071	612	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272475.1	s__Novosphingobium sp000272475	79.627	421	1189	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	79.6022	477	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_000281975.1	s__Novosphingobium sp000281975	79.5943	483	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742225.1	s__Novosphingobium resinovorum	79.4656	527	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	79.4617	461	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341845.1	s__Novosphingobium sp004341845	79.3458	480	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421325.1	s__Novosphingobium sp001421325	79.2283	463	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	79.2251	438	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	79.1902	427	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.01	453	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211435.1	s__Novosphingobium sp004211435	78.9332	375	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019075875.1	s__Novosphingobium sp019075875	78.7654	408	1189	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 15:28:05,401] [INFO] GTDB search result was written to GCF_014196615.1_ASM1419661v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:05,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:05,409] [INFO] DFAST_QC result json was written to GCF_014196615.1_ASM1419661v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:05,409] [INFO] DFAST_QC completed!
[2024-01-24 15:28:05,409] [INFO] Total running time: 0h1m26s