[2024-01-25 18:02:35,543] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:35,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:35,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg954ef916-b8d0-4a0a-aacc-9985ee260ce0/dqc_reference
[2024-01-25 18:02:36,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:36,641] [INFO] Task started: Prodigal
[2024-01-25 18:02:36,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ee3bf2f-2988-4409-972b-606794f112bc/GCF_021227995.1_ASM2122799v1_genomic.fna.gz | prodigal -d GCF_021227995.1_ASM2122799v1_genomic.fna/cds.fna -a GCF_021227995.1_ASM2122799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:51,485] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:51,486] [INFO] Task started: HMMsearch
[2024-01-25 18:02:51,486] [INFO] Running command: hmmsearch --tblout GCF_021227995.1_ASM2122799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg954ef916-b8d0-4a0a-aacc-9985ee260ce0/dqc_reference/reference_markers.hmm GCF_021227995.1_ASM2122799v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:51,866] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:51,867] [INFO] Found 6/6 markers.
[2024-01-25 18:02:51,920] [INFO] Query marker FASTA was written to GCF_021227995.1_ASM2122799v1_genomic.fna/markers.fasta
[2024-01-25 18:02:51,920] [INFO] Task started: Blastn
[2024-01-25 18:02:51,920] [INFO] Running command: blastn -query GCF_021227995.1_ASM2122799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg954ef916-b8d0-4a0a-aacc-9985ee260ce0/dqc_reference/reference_markers.fasta -out GCF_021227995.1_ASM2122799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:52,970] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:52,980] [INFO] Selected 17 target genomes.
[2024-01-25 18:02:52,980] [INFO] Target genome list was writen to GCF_021227995.1_ASM2122799v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:52,992] [INFO] Task started: fastANI
[2024-01-25 18:02:52,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ee3bf2f-2988-4409-972b-606794f112bc/GCF_021227995.1_ASM2122799v1_genomic.fna.gz --refList GCF_021227995.1_ASM2122799v1_genomic.fna/target_genomes.txt --output GCF_021227995.1_ASM2122799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:10,151] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:10,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg954ef916-b8d0-4a0a-aacc-9985ee260ce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:10,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg954ef916-b8d0-4a0a-aacc-9985ee260ce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:10,163] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:03:10,163] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:03:10,163] [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 guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	85.9186	1139	1899	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	83.0598	976	1899	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	82.4888	885	1899	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	82.0479	672	1899	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	82.0129	768	1899	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	81.4407	621	1899	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	81.4289	605	1899	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	81.3662	728	1899	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	81.3123	669	1899	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	81.2135	635	1899	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	81.1608	745	1899	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.8639	681	1899	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.8249	740	1899	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	80.7348	605	1899	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.849	563	1899	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.6466	566	1899	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.6203	537	1899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:10,164] [INFO] DFAST Taxonomy check result was written to GCF_021227995.1_ASM2122799v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:10,165] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:10,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:10,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg954ef916-b8d0-4a0a-aacc-9985ee260ce0/dqc_reference/checkm_data
[2024-01-25 18:03:10,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:10,219] [INFO] Task started: CheckM
[2024-01-25 18:03:10,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021227995.1_ASM2122799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021227995.1_ASM2122799v1_genomic.fna/checkm_input GCF_021227995.1_ASM2122799v1_genomic.fna/checkm_result
[2024-01-25 18:03:56,247] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:56,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:56,266] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:56,266] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:56,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021227995.1_ASM2122799v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:56,267] [INFO] Task started: Blastn
[2024-01-25 18:03:56,267] [INFO] Running command: blastn -query GCF_021227995.1_ASM2122799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg954ef916-b8d0-4a0a-aacc-9985ee260ce0/dqc_reference/reference_markers_gtdb.fasta -out GCF_021227995.1_ASM2122799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:58,153] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:58,156] [INFO] Selected 12 target genomes.
[2024-01-25 18:03:58,156] [INFO] Target genome list was writen to GCF_021227995.1_ASM2122799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:58,165] [INFO] Task started: fastANI
[2024-01-25 18:03:58,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ee3bf2f-2988-4409-972b-606794f112bc/GCF_021227995.1_ASM2122799v1_genomic.fna.gz --refList GCF_021227995.1_ASM2122799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021227995.1_ASM2122799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:12,987] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:12,996] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:04:12,996] [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_001742225.1	s__Novosphingobium resinovorum	86.4614	1182	1899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_002896965.1	s__Novosphingobium guangzhouense	85.8885	1142	1899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281975.1	s__Novosphingobium sp000281975	84.4794	1061	1899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000876675.2	s__Novosphingobium sp000876675	83.1155	1033	1899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856825.1	s__Novosphingobium sp009856825	82.4876	884	1899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	82.4722	900	1899	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	82.3416	879	1899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_002149965.1	s__Novosphingobium panipatense	82.2255	897	1899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_002916655.1	s__Novosphingobium sp002916655	82.19	736	1899	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	81.3665	728	1899	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	81.1398	658	1899	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	80.492	674	1899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:12,997] [INFO] GTDB search result was written to GCF_021227995.1_ASM2122799v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:12,998] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:13,001] [INFO] DFAST_QC result json was written to GCF_021227995.1_ASM2122799v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:13,001] [INFO] DFAST_QC completed!
[2024-01-25 18:04:13,001] [INFO] Total running time: 0h1m37s