[2024-01-25 19:44:05,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:05,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:05,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c002159-65d3-4cd5-9fac-71d188681c34/dqc_reference
[2024-01-25 19:44:06,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:06,847] [INFO] Task started: Prodigal
[2024-01-25 19:44:06,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg86d87668-8c0e-4a39-83af-7165007daf13/GCF_014640675.1_ASM1464067v1_genomic.fna.gz | prodigal -d GCF_014640675.1_ASM1464067v1_genomic.fna/cds.fna -a GCF_014640675.1_ASM1464067v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:17,860] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:17,861] [INFO] Task started: HMMsearch
[2024-01-25 19:44:17,861] [INFO] Running command: hmmsearch --tblout GCF_014640675.1_ASM1464067v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c002159-65d3-4cd5-9fac-71d188681c34/dqc_reference/reference_markers.hmm GCF_014640675.1_ASM1464067v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:18,138] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:18,139] [INFO] Found 6/6 markers.
[2024-01-25 19:44:18,208] [INFO] Query marker FASTA was written to GCF_014640675.1_ASM1464067v1_genomic.fna/markers.fasta
[2024-01-25 19:44:18,208] [INFO] Task started: Blastn
[2024-01-25 19:44:18,208] [INFO] Running command: blastn -query GCF_014640675.1_ASM1464067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c002159-65d3-4cd5-9fac-71d188681c34/dqc_reference/reference_markers.fasta -out GCF_014640675.1_ASM1464067v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:19,206] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:19,210] [INFO] Selected 16 target genomes.
[2024-01-25 19:44:19,210] [INFO] Target genome list was writen to GCF_014640675.1_ASM1464067v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:19,220] [INFO] Task started: fastANI
[2024-01-25 19:44:19,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d87668-8c0e-4a39-83af-7165007daf13/GCF_014640675.1_ASM1464067v1_genomic.fna.gz --refList GCF_014640675.1_ASM1464067v1_genomic.fna/target_genomes.txt --output GCF_014640675.1_ASM1464067v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:33,898] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:33,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c002159-65d3-4cd5-9fac-71d188681c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:33,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c002159-65d3-4cd5-9fac-71d188681c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:33,909] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:33,910] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:33,910] [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 endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	100.0	1390	1396	95	conclusive
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	82.2	669	1396	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	82.1567	670	1396	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	82.1391	682	1396	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	81.2303	662	1396	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	81.1849	665	1396	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	80.7374	566	1396	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	80.6653	560	1396	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.3158	564	1396	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.1712	541	1396	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	80.1473	519	1396	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	80.1434	550	1396	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.5826	507	1396	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.5381	467	1396	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	79.3152	469	1396	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.1468	450	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:33,911] [INFO] DFAST Taxonomy check result was written to GCF_014640675.1_ASM1464067v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:33,911] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:33,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:33,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c002159-65d3-4cd5-9fac-71d188681c34/dqc_reference/checkm_data
[2024-01-25 19:44:33,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:33,954] [INFO] Task started: CheckM
[2024-01-25 19:44:33,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640675.1_ASM1464067v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640675.1_ASM1464067v1_genomic.fna/checkm_input GCF_014640675.1_ASM1464067v1_genomic.fna/checkm_result
[2024-01-25 19:45:08,019] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:08,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:08,035] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:08,035] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:08,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640675.1_ASM1464067v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:08,036] [INFO] Task started: Blastn
[2024-01-25 19:45:08,036] [INFO] Running command: blastn -query GCF_014640675.1_ASM1464067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c002159-65d3-4cd5-9fac-71d188681c34/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640675.1_ASM1464067v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:09,763] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:09,766] [INFO] Selected 17 target genomes.
[2024-01-25 19:45:09,766] [INFO] Target genome list was writen to GCF_014640675.1_ASM1464067v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:09,794] [INFO] Task started: fastANI
[2024-01-25 19:45:09,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d87668-8c0e-4a39-83af-7165007daf13/GCF_014640675.1_ASM1464067v1_genomic.fna.gz --refList GCF_014640675.1_ASM1464067v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640675.1_ASM1464067v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:27,270] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:27,281] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:27,281] [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_014640675.1	s__Novosphingobium endophyticum	100.0	1390	1396	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_000767465.1	s__Novosphingobium pentaromativorans	82.1578	680	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_900168325.1	s__Novosphingobium mathurense	82.1567	670	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_900113255.1	s__Novosphingobium sp900113255	81.8771	592	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	81.7345	616	1396	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	81.2187	663	1396	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	81.1751	666	1396	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	81.1214	653	1396	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	81.0972	596	1396	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	81.0855	564	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149965.1	s__Novosphingobium panipatense	80.9461	636	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_006874585.1	s__Novosphingobium sp006874585	80.7925	666	1396	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	80.7781	632	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_015865035.1	s__Novosphingobium sp015865035	80.7374	566	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298105.1	s__Novosphingobium sp001298105	80.6635	596	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCF_902706195.1	s__Novosphingobium sp902706195	80.2849	596	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009856825.1	s__Novosphingobium sp009856825	80.1434	550	1396	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 19:45:27,282] [INFO] GTDB search result was written to GCF_014640675.1_ASM1464067v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:27,283] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:27,286] [INFO] DFAST_QC result json was written to GCF_014640675.1_ASM1464067v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:27,286] [INFO] DFAST_QC completed!
[2024-01-25 19:45:27,286] [INFO] Total running time: 0h1m22s