[2024-01-25 18:54:35,665] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:35,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:35,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg941fc9a4-c201-4c28-8b34-691a2d7ad7d5/dqc_reference
[2024-01-25 18:54:36,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:36,823] [INFO] Task started: Prodigal
[2024-01-25 18:54:36,823] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf80ccdc-f5f1-4cc7-a978-110cca1cca4e/GCF_014639875.1_ASM1463987v1_genomic.fna.gz | prodigal -d GCF_014639875.1_ASM1463987v1_genomic.fna/cds.fna -a GCF_014639875.1_ASM1463987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:47,418] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:47,418] [INFO] Task started: HMMsearch
[2024-01-25 18:54:47,418] [INFO] Running command: hmmsearch --tblout GCF_014639875.1_ASM1463987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg941fc9a4-c201-4c28-8b34-691a2d7ad7d5/dqc_reference/reference_markers.hmm GCF_014639875.1_ASM1463987v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:47,629] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:47,630] [INFO] Found 6/6 markers.
[2024-01-25 18:54:47,660] [INFO] Query marker FASTA was written to GCF_014639875.1_ASM1463987v1_genomic.fna/markers.fasta
[2024-01-25 18:54:47,660] [INFO] Task started: Blastn
[2024-01-25 18:54:47,660] [INFO] Running command: blastn -query GCF_014639875.1_ASM1463987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg941fc9a4-c201-4c28-8b34-691a2d7ad7d5/dqc_reference/reference_markers.fasta -out GCF_014639875.1_ASM1463987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:48,511] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:48,514] [INFO] Selected 23 target genomes.
[2024-01-25 18:54:48,514] [INFO] Target genome list was writen to GCF_014639875.1_ASM1463987v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:48,527] [INFO] Task started: fastANI
[2024-01-25 18:54:48,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf80ccdc-f5f1-4cc7-a978-110cca1cca4e/GCF_014639875.1_ASM1463987v1_genomic.fna.gz --refList GCF_014639875.1_ASM1463987v1_genomic.fna/target_genomes.txt --output GCF_014639875.1_ASM1463987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:05,610] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:05,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg941fc9a4-c201-4c28-8b34-691a2d7ad7d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:05,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg941fc9a4-c201-4c28-8b34-691a2d7ad7d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:05,627] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:05,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:05,627] [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
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	100.0	1224	1225	95	conclusive
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	85.9023	939	1225	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	78.3089	350	1225	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	78.1161	309	1225	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.0844	357	1225	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.0082	313	1225	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	77.9477	295	1225	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.8939	271	1225	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.7285	263	1225	95	below_threshold
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	77.7094	305	1225	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.7068	286	1225	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	77.6609	222	1225	95	below_threshold
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	77.6461	265	1225	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	77.6241	299	1225	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	77.6137	270	1225	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.6135	287	1225	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.5614	291	1225	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.4997	271	1225	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	77.4871	298	1225	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.4853	255	1225	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	77.4753	266	1225	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.4362	239	1225	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	77.376	292	1225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:05,628] [INFO] DFAST Taxonomy check result was written to GCF_014639875.1_ASM1463987v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:05,629] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:05,629] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:05,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg941fc9a4-c201-4c28-8b34-691a2d7ad7d5/dqc_reference/checkm_data
[2024-01-25 18:55:05,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:05,676] [INFO] Task started: CheckM
[2024-01-25 18:55:05,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639875.1_ASM1463987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639875.1_ASM1463987v1_genomic.fna/checkm_input GCF_014639875.1_ASM1463987v1_genomic.fna/checkm_result
[2024-01-25 18:55:38,962] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:38,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:38,990] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:38,991] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:38,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639875.1_ASM1463987v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:38,991] [INFO] Task started: Blastn
[2024-01-25 18:55:38,991] [INFO] Running command: blastn -query GCF_014639875.1_ASM1463987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg941fc9a4-c201-4c28-8b34-691a2d7ad7d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639875.1_ASM1463987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:40,690] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:40,693] [INFO] Selected 9 target genomes.
[2024-01-25 18:55:40,693] [INFO] Target genome list was writen to GCF_014639875.1_ASM1463987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:40,702] [INFO] Task started: fastANI
[2024-01-25 18:55:40,702] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf80ccdc-f5f1-4cc7-a978-110cca1cca4e/GCF_014639875.1_ASM1463987v1_genomic.fna.gz --refList GCF_014639875.1_ASM1463987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639875.1_ASM1463987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:49,059] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:49,066] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:49,066] [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_014639875.1	s__Blastomonas aquatica	100.0	1224	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003431825.1	s__Blastomonas fulva	85.9265	938	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	98.01	97.97	0.88	0.85	3	-
GCF_000786215.1	s__Blastomonas sp000786215	84.458	875	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331245.1	s__Blastomonas sp000331245	84.38	849	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000503195.1	s__Blastomonas sp000503195	83.364	819	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.00	97.00	0.84	0.84	2	-
GCF_013607875.1	s__Blastomonas ursincola	83.3155	856	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.82	97.14	0.88	0.79	7	-
GCA_001555775.1	s__Blastomonas delafieldii_A	83.3039	800	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	99.74	98.25	0.90	0.81	22	-
GCF_003201955.1	s__Blastomonas natatoria	82.7857	837	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677335.1	s__Erythrobacter dokdonensis	77.6135	287	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:49,067] [INFO] GTDB search result was written to GCF_014639875.1_ASM1463987v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:49,067] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:49,071] [INFO] DFAST_QC result json was written to GCF_014639875.1_ASM1463987v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:49,071] [INFO] DFAST_QC completed!
[2024-01-25 18:55:49,071] [INFO] Total running time: 0h1m13s