[2024-01-24 15:18:38,640] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e949582-ad6b-449a-8ab9-548e1a6812e7/dqc_reference
[2024-01-24 15:18:40,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,013] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg4aee105a-577c-49b5-9c1e-dd424589f05a/GCF_014230305.1_ASM1423030v1_genomic.fna.gz | prodigal -d GCF_014230305.1_ASM1423030v1_genomic.fna/cds.fna -a GCF_014230305.1_ASM1423030v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:52,154] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:52,154] [INFO] Task started: HMMsearch
[2024-01-24 15:18:52,154] [INFO] Running command: hmmsearch --tblout GCF_014230305.1_ASM1423030v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e949582-ad6b-449a-8ab9-548e1a6812e7/dqc_reference/reference_markers.hmm GCF_014230305.1_ASM1423030v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:52,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:52,442] [INFO] Found 6/6 markers.
[2024-01-24 15:18:52,477] [INFO] Query marker FASTA was written to GCF_014230305.1_ASM1423030v1_genomic.fna/markers.fasta
[2024-01-24 15:18:52,478] [INFO] Task started: Blastn
[2024-01-24 15:18:52,478] [INFO] Running command: blastn -query GCF_014230305.1_ASM1423030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e949582-ad6b-449a-8ab9-548e1a6812e7/dqc_reference/reference_markers.fasta -out GCF_014230305.1_ASM1423030v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:53,524] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:53,528] [INFO] Selected 18 target genomes.
[2024-01-24 15:18:53,529] [INFO] Target genome list was writen to GCF_014230305.1_ASM1423030v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:53,536] [INFO] Task started: fastANI
[2024-01-24 15:18:53,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aee105a-577c-49b5-9c1e-dd424589f05a/GCF_014230305.1_ASM1423030v1_genomic.fna.gz --refList GCF_014230305.1_ASM1423030v1_genomic.fna/target_genomes.txt --output GCF_014230305.1_ASM1423030v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:09,792] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:09,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e949582-ad6b-449a-8ab9-548e1a6812e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:09,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e949582-ad6b-449a-8ab9-548e1a6812e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:09,808] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:09,808] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:09,809] [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 aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	100.0	1340	1342	95	conclusive
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	85.3185	847	1342	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	81.5969	597	1342	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	80.5347	536	1342	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	80.3369	501	1342	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	80.2704	511	1342	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	80.2246	521	1342	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	80.0828	555	1342	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	80.0543	526	1342	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	80.0177	518	1342	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.6626	454	1342	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	79.3199	455	1342	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.2429	421	1342	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	79.0838	453	1342	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	79.0015	407	1342	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	78.9714	438	1342	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.8642	402	1342	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.436	364	1342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:09,810] [INFO] DFAST Taxonomy check result was written to GCF_014230305.1_ASM1423030v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:09,811] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:09,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:09,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e949582-ad6b-449a-8ab9-548e1a6812e7/dqc_reference/checkm_data
[2024-01-24 15:19:09,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:09,854] [INFO] Task started: CheckM
[2024-01-24 15:19:09,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014230305.1_ASM1423030v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014230305.1_ASM1423030v1_genomic.fna/checkm_input GCF_014230305.1_ASM1423030v1_genomic.fna/checkm_result
[2024-01-24 15:19:52,391] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:52,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:52,413] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:52,414] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:52,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014230305.1_ASM1423030v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:52,415] [INFO] Task started: Blastn
[2024-01-24 15:19:52,415] [INFO] Running command: blastn -query GCF_014230305.1_ASM1423030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e949582-ad6b-449a-8ab9-548e1a6812e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014230305.1_ASM1423030v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:54,364] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:54,369] [INFO] Selected 14 target genomes.
[2024-01-24 15:19:54,369] [INFO] Target genome list was writen to GCF_014230305.1_ASM1423030v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:54,379] [INFO] Task started: fastANI
[2024-01-24 15:19:54,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aee105a-577c-49b5-9c1e-dd424589f05a/GCF_014230305.1_ASM1423030v1_genomic.fna.gz --refList GCF_014230305.1_ASM1423030v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014230305.1_ASM1423030v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:05,967] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:05,986] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:05,987] [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_014230305.1	s__Novosphingobium aerophilum	100.0	1340	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.68	98.68	0.90	0.90	2	conclusive
GCF_014230355.1	s__Novosphingobium piscinae	85.3185	847	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230315.1	s__Novosphingobium flavum	81.5808	599	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719755.1	s__Novosphingobium sp016719755	80.6207	513	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCA_013791705.1	s__Novosphingobium sp013791705	80.425	439	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.87	99.87	0.91	0.91	2	-
GCA_017302615.1	s__Novosphingobium sp017302615	80.3011	494	1342	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	80.1518	515	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_014652615.1	s__Novosphingobium arvoryzae	80.0651	525	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000807925.1	s__Novosphingobium subterraneum	79.9969	520	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCA_004211435.1	s__Novosphingobium sp004211435	79.9684	481	1342	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	79.8343	494	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454125.1	s__Novosphingobium sp002454125	79.5565	412	1342	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	79.4041	453	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	78.6466	386	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:05,989] [INFO] GTDB search result was written to GCF_014230305.1_ASM1423030v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:05,989] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:05,993] [INFO] DFAST_QC result json was written to GCF_014230305.1_ASM1423030v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:05,993] [INFO] DFAST_QC completed!
[2024-01-24 15:20:05,993] [INFO] Total running time: 0h1m27s