[2024-01-24 13:36:57,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:57,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:57,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4819ddb-ec6e-473a-a764-59c51c5e5d03/dqc_reference
[2024-01-24 13:36:58,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:58,827] [INFO] Task started: Prodigal
[2024-01-24 13:36:58,827] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6df8c40-7a8a-45b0-b9cb-9ee6e12b9788/GCF_014652615.1_ASM1465261v1_genomic.fna.gz | prodigal -d GCF_014652615.1_ASM1465261v1_genomic.fna/cds.fna -a GCF_014652615.1_ASM1465261v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:09,370] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:09,370] [INFO] Task started: HMMsearch
[2024-01-24 13:37:09,370] [INFO] Running command: hmmsearch --tblout GCF_014652615.1_ASM1465261v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4819ddb-ec6e-473a-a764-59c51c5e5d03/dqc_reference/reference_markers.hmm GCF_014652615.1_ASM1465261v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:09,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:09,662] [INFO] Found 6/6 markers.
[2024-01-24 13:37:09,710] [INFO] Query marker FASTA was written to GCF_014652615.1_ASM1465261v1_genomic.fna/markers.fasta
[2024-01-24 13:37:09,711] [INFO] Task started: Blastn
[2024-01-24 13:37:09,711] [INFO] Running command: blastn -query GCF_014652615.1_ASM1465261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4819ddb-ec6e-473a-a764-59c51c5e5d03/dqc_reference/reference_markers.fasta -out GCF_014652615.1_ASM1465261v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:10,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:10,739] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:10,739] [INFO] Target genome list was writen to GCF_014652615.1_ASM1465261v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:10,749] [INFO] Task started: fastANI
[2024-01-24 13:37:10,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6df8c40-7a8a-45b0-b9cb-9ee6e12b9788/GCF_014652615.1_ASM1465261v1_genomic.fna.gz --refList GCF_014652615.1_ASM1465261v1_genomic.fna/target_genomes.txt --output GCF_014652615.1_ASM1465261v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:26,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:26,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4819ddb-ec6e-473a-a764-59c51c5e5d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:26,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4819ddb-ec6e-473a-a764-59c51c5e5d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:26,479] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:26,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:26,480] [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 arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	100.0	1084	1084	95	conclusive
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	80.8857	579	1084	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	80.6948	580	1084	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	80.2338	516	1084	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	80.2313	469	1084	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	80.1552	492	1084	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	80.1277	525	1084	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	80.0265	495	1084	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	79.8309	517	1084	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	79.7562	500	1084	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	79.7049	521	1084	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	79.6862	486	1084	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.5638	453	1084	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	79.2013	472	1084	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.0	354	1084	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.8026	419	1084	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	78.559	350	1084	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.4874	397	1084	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	78.3007	340	1084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:26,481] [INFO] DFAST Taxonomy check result was written to GCF_014652615.1_ASM1465261v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:26,482] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:26,482] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:26,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4819ddb-ec6e-473a-a764-59c51c5e5d03/dqc_reference/checkm_data
[2024-01-24 13:37:26,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:26,520] [INFO] Task started: CheckM
[2024-01-24 13:37:26,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652615.1_ASM1465261v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652615.1_ASM1465261v1_genomic.fna/checkm_input GCF_014652615.1_ASM1465261v1_genomic.fna/checkm_result
[2024-01-24 13:38:01,695] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:01,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:01,717] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:01,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:01,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652615.1_ASM1465261v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:01,718] [INFO] Task started: Blastn
[2024-01-24 13:38:01,718] [INFO] Running command: blastn -query GCF_014652615.1_ASM1465261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4819ddb-ec6e-473a-a764-59c51c5e5d03/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652615.1_ASM1465261v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:03,506] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:03,510] [INFO] Selected 21 target genomes.
[2024-01-24 13:38:03,510] [INFO] Target genome list was writen to GCF_014652615.1_ASM1465261v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:03,864] [INFO] Task started: fastANI
[2024-01-24 13:38:03,864] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6df8c40-7a8a-45b0-b9cb-9ee6e12b9788/GCF_014652615.1_ASM1465261v1_genomic.fna.gz --refList GCF_014652615.1_ASM1465261v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652615.1_ASM1465261v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:20,102] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:20,123] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:20,123] [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_014652615.1	s__Novosphingobium arvoryzae	100.0	1084	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016719755.1	s__Novosphingobium sp016719755	82.4788	693	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCA_017302615.1	s__Novosphingobium sp017302615	82.2694	669	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198665.1	s__Novosphingobium sp002198665	81.5197	682	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657645.1	s__Novosphingobium sp015657645	81.4049	540	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926135.1	s__Novosphingobium sp009926135	81.1157	575	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855555.1	s__Novosphingobium sp002855555	80.9172	500	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141325.1	s__Novosphingobium sp013141325	80.7693	471	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440635.1	s__Novosphingobium sp002440635	80.7649	595	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813245.1	s__Novosphingobium kunmingense	80.684	581	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822005.1	s__Novosphingobium sp013822005	80.5928	446	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240895.1	s__Novosphingobium sp018240895	79.8308	498	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694345.1	s__Novosphingobium jiangmenense	79.8148	519	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927405.1	s__Novosphingobium olei	79.7534	501	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003454795.1	s__Novosphingobium sp003454795	79.7502	511	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	79.7118	486	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012641335.1	s__Novosphingobium sp012641335	79.5063	475	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971065.1	s__Novosphingobium sp018971065	79.3845	434	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176395.1	s__Novosphingobium sp900176395	79.2468	468	1084	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	79.2259	456	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_000876675.2	s__Novosphingobium sp000876675	79.103	440	1084	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 13:38:20,125] [INFO] GTDB search result was written to GCF_014652615.1_ASM1465261v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:20,126] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:20,134] [INFO] DFAST_QC result json was written to GCF_014652615.1_ASM1465261v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:20,134] [INFO] DFAST_QC completed!
[2024-01-24 13:38:20,134] [INFO] Total running time: 0h1m23s