[2024-01-24 13:46:01,674] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d3bf375-68d7-458e-bbef-30f31a93dca7/dqc_reference
[2024-01-24 13:46:03,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:03,097] [INFO] Task started: Prodigal
[2024-01-24 13:46:03,097] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9ab1a34-22ae-4ad4-b111-a546ce44ffc5/GCF_014652555.1_ASM1465255v1_genomic.fna.gz | prodigal -d GCF_014652555.1_ASM1465255v1_genomic.fna/cds.fna -a GCF_014652555.1_ASM1465255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:14,638] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:14,639] [INFO] Task started: HMMsearch
[2024-01-24 13:46:14,639] [INFO] Running command: hmmsearch --tblout GCF_014652555.1_ASM1465255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d3bf375-68d7-458e-bbef-30f31a93dca7/dqc_reference/reference_markers.hmm GCF_014652555.1_ASM1465255v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:14,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:14,911] [INFO] Found 6/6 markers.
[2024-01-24 13:46:14,949] [INFO] Query marker FASTA was written to GCF_014652555.1_ASM1465255v1_genomic.fna/markers.fasta
[2024-01-24 13:46:14,949] [INFO] Task started: Blastn
[2024-01-24 13:46:14,949] [INFO] Running command: blastn -query GCF_014652555.1_ASM1465255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d3bf375-68d7-458e-bbef-30f31a93dca7/dqc_reference/reference_markers.fasta -out GCF_014652555.1_ASM1465255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:15,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:15,961] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:15,961] [INFO] Target genome list was writen to GCF_014652555.1_ASM1465255v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:15,975] [INFO] Task started: fastANI
[2024-01-24 13:46:15,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ab1a34-22ae-4ad4-b111-a546ce44ffc5/GCF_014652555.1_ASM1465255v1_genomic.fna.gz --refList GCF_014652555.1_ASM1465255v1_genomic.fna/target_genomes.txt --output GCF_014652555.1_ASM1465255v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:34,089] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:34,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d3bf375-68d7-458e-bbef-30f31a93dca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:34,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d3bf375-68d7-458e-bbef-30f31a93dca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:34,107] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:34,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:34,107] [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 colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	100.0	1222	1225	95	conclusive
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	80.9602	585	1225	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	80.2505	510	1225	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	80.1831	513	1225	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	80.1821	583	1225	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	80.1163	569	1225	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	80.0567	509	1225	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.0355	543	1225	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	79.7513	458	1225	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	79.6478	518	1225	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	79.6451	527	1225	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	79.5474	503	1225	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.5231	486	1225	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	79.5112	470	1225	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.5096	502	1225	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	79.4797	459	1225	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	79.3412	429	1225	95	below_threshold
Novosphingobium fluoreni	strain=DSM 27568	GCA_014196615.1	1391222	1391222	type	True	79.2836	433	1225	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.1099	470	1225	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	78.8891	408	1225	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	78.8753	422	1225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:34,110] [INFO] DFAST Taxonomy check result was written to GCF_014652555.1_ASM1465255v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:34,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:34,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:34,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d3bf375-68d7-458e-bbef-30f31a93dca7/dqc_reference/checkm_data
[2024-01-24 13:46:34,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:34,149] [INFO] Task started: CheckM
[2024-01-24 13:46:34,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652555.1_ASM1465255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652555.1_ASM1465255v1_genomic.fna/checkm_input GCF_014652555.1_ASM1465255v1_genomic.fna/checkm_result
[2024-01-24 13:47:10,631] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:10,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:10,657] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:10,658] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:10,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652555.1_ASM1465255v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:10,658] [INFO] Task started: Blastn
[2024-01-24 13:47:10,658] [INFO] Running command: blastn -query GCF_014652555.1_ASM1465255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d3bf375-68d7-458e-bbef-30f31a93dca7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652555.1_ASM1465255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:12,575] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:12,611] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:12,612] [INFO] Target genome list was writen to GCF_014652555.1_ASM1465255v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:12,655] [INFO] Task started: fastANI
[2024-01-24 13:47:12,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ab1a34-22ae-4ad4-b111-a546ce44ffc5/GCF_014652555.1_ASM1465255v1_genomic.fna.gz --refList GCF_014652555.1_ASM1465255v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652555.1_ASM1465255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:30,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:30,478] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:30,479] [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_014652555.1	s__Novosphingobium colocasiae	100.0	1222	1225	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_001590985.1	s__Novosphingobium naphthalenivorans	80.9458	586	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113255.1	s__Novosphingobium sp900113255	80.8291	590	1225	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	80.5298	605	1225	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	80.5005	573	1225	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	80.2951	584	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_004342985.1	s__Novosphingobium sp004342985	80.2691	567	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.88	97.88	0.88	0.88	2	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	80.2586	572	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640675.1	s__Novosphingobium endophyticum	80.257	509	1225	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	80.2531	529	1225	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	80.2383	545	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCF_001046635.1	s__Novosphingobium barchaimii	80.1857	583	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445125.1	s__Novosphingobium lindaniclasticum	80.1436	517	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802225.1	s__Novosphingobium malaysiense	80.0549	510	1225	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	79.9619	517	1225	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	79.7406	535	1225	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	79.4505	511	1225	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	78.5925	325	1225	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 13:47:30,480] [INFO] GTDB search result was written to GCF_014652555.1_ASM1465255v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:30,481] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:30,485] [INFO] DFAST_QC result json was written to GCF_014652555.1_ASM1465255v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:30,485] [INFO] DFAST_QC completed!
[2024-01-24 13:47:30,485] [INFO] Total running time: 0h1m29s