[2024-01-24 10:57:26,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg56a3e422-1113-40ee-a159-8b7abf693431/dqc_reference
[2024-01-24 10:57:28,189] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,190] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg8da02d73-78f4-44c6-97ad-5c8b5a7ff7fe/GCF_018491765.1_ASM1849176v1_genomic.fna.gz | prodigal -d GCF_018491765.1_ASM1849176v1_genomic.fna/cds.fna -a GCF_018491765.1_ASM1849176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:45,450] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:45,450] [INFO] Task started: HMMsearch
[2024-01-24 10:57:45,450] [INFO] Running command: hmmsearch --tblout GCF_018491765.1_ASM1849176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56a3e422-1113-40ee-a159-8b7abf693431/dqc_reference/reference_markers.hmm GCF_018491765.1_ASM1849176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:45,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:45,805] [INFO] Found 6/6 markers.
[2024-01-24 10:57:45,851] [INFO] Query marker FASTA was written to GCF_018491765.1_ASM1849176v1_genomic.fna/markers.fasta
[2024-01-24 10:57:45,852] [INFO] Task started: Blastn
[2024-01-24 10:57:45,852] [INFO] Running command: blastn -query GCF_018491765.1_ASM1849176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56a3e422-1113-40ee-a159-8b7abf693431/dqc_reference/reference_markers.fasta -out GCF_018491765.1_ASM1849176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:46,958] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:46,961] [INFO] Selected 14 target genomes.
[2024-01-24 10:57:46,962] [INFO] Target genome list was writen to GCF_018491765.1_ASM1849176v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:46,992] [INFO] Task started: fastANI
[2024-01-24 10:57:46,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg8da02d73-78f4-44c6-97ad-5c8b5a7ff7fe/GCF_018491765.1_ASM1849176v1_genomic.fna.gz --refList GCF_018491765.1_ASM1849176v1_genomic.fna/target_genomes.txt --output GCF_018491765.1_ASM1849176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,969] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56a3e422-1113-40ee-a159-8b7abf693431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56a3e422-1113-40ee-a159-8b7abf693431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,980] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:01,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:01,981] [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 profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	100.0	1865	1870	95	conclusive
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	84.4824	1016	1870	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	82.9588	870	1870	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	80.9638	678	1870	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	80.8781	641	1870	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	80.8054	643	1870	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	80.7162	654	1870	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.5798	640	1870	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	80.5366	698	1870	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	80.43	606	1870	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.7523	510	1870	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.2618	538	1870	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.963	509	1870	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.338	392	1870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,997] [INFO] DFAST Taxonomy check result was written to GCF_018491765.1_ASM1849176v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56a3e422-1113-40ee-a159-8b7abf693431/dqc_reference/checkm_data
[2024-01-24 10:58:02,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:02,055] [INFO] Task started: CheckM
[2024-01-24 10:58:02,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018491765.1_ASM1849176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018491765.1_ASM1849176v1_genomic.fna/checkm_input GCF_018491765.1_ASM1849176v1_genomic.fna/checkm_result
[2024-01-24 10:58:50,475] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:50,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:50,495] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:50,495] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:50,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018491765.1_ASM1849176v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:50,495] [INFO] Task started: Blastn
[2024-01-24 10:58:50,495] [INFO] Running command: blastn -query GCF_018491765.1_ASM1849176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56a3e422-1113-40ee-a159-8b7abf693431/dqc_reference/reference_markers_gtdb.fasta -out GCF_018491765.1_ASM1849176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:52,505] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:52,510] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:52,510] [INFO] Target genome list was writen to GCF_018491765.1_ASM1849176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:52,540] [INFO] Task started: fastANI
[2024-01-24 10:58:52,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg8da02d73-78f4-44c6-97ad-5c8b5a7ff7fe/GCF_018491765.1_ASM1849176v1_genomic.fna.gz --refList GCF_018491765.1_ASM1849176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018491765.1_ASM1849176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:06,070] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:06,082] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:06,082] [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_018491765.1	s__Novosphingobium profundi	100.0	1865	1870	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_018417475.1	s__Novosphingobium sp000813185	84.4779	1016	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_008107685.1	s__Novosphingobium sp008107685	83.2302	911	1870	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	82.9927	868	1870	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	81.0957	773	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	80.9914	675	1870	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	80.5532	641	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	80.5321	744	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002896965.1	s__Novosphingobium guangzhouense	80.5278	699	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342985.1	s__Novosphingobium sp004342985	80.5264	703	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.88	97.88	0.88	0.88	2	-
GCF_000802225.1	s__Novosphingobium malaysiense	80.4303	606	1870	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	80.2719	623	1870	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 10:59:06,084] [INFO] GTDB search result was written to GCF_018491765.1_ASM1849176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:06,085] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:06,089] [INFO] DFAST_QC result json was written to GCF_018491765.1_ASM1849176v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:06,089] [INFO] DFAST_QC completed!
[2024-01-24 10:59:06,089] [INFO] Total running time: 0h1m39s