[2024-01-24 14:02:47,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:47,180] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:47,180] [INFO] DQC Reference Directory: /var/lib/cwl/stgd04f83ad-41f8-402d-93d3-0470cb08bb01/dqc_reference
[2024-01-24 14:02:48,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:48,504] [INFO] Task started: Prodigal
[2024-01-24 14:02:48,505] [INFO] Running command: gunzip -c /var/lib/cwl/stg71f6c5b1-29e2-46ec-8208-a88356f124b8/GCF_023006325.1_ASM2300632v1_genomic.fna.gz | prodigal -d GCF_023006325.1_ASM2300632v1_genomic.fna/cds.fna -a GCF_023006325.1_ASM2300632v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:02:59,745] [INFO] Task succeeded: Prodigal
[2024-01-24 14:02:59,746] [INFO] Task started: HMMsearch
[2024-01-24 14:02:59,746] [INFO] Running command: hmmsearch --tblout GCF_023006325.1_ASM2300632v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd04f83ad-41f8-402d-93d3-0470cb08bb01/dqc_reference/reference_markers.hmm GCF_023006325.1_ASM2300632v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:00,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:00,024] [INFO] Found 6/6 markers.
[2024-01-24 14:03:00,062] [INFO] Query marker FASTA was written to GCF_023006325.1_ASM2300632v1_genomic.fna/markers.fasta
[2024-01-24 14:03:00,062] [INFO] Task started: Blastn
[2024-01-24 14:03:00,063] [INFO] Running command: blastn -query GCF_023006325.1_ASM2300632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd04f83ad-41f8-402d-93d3-0470cb08bb01/dqc_reference/reference_markers.fasta -out GCF_023006325.1_ASM2300632v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:00,952] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:00,956] [INFO] Selected 18 target genomes.
[2024-01-24 14:03:00,956] [INFO] Target genome list was writen to GCF_023006325.1_ASM2300632v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:00,966] [INFO] Task started: fastANI
[2024-01-24 14:03:00,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f6c5b1-29e2-46ec-8208-a88356f124b8/GCF_023006325.1_ASM2300632v1_genomic.fna.gz --refList GCF_023006325.1_ASM2300632v1_genomic.fna/target_genomes.txt --output GCF_023006325.1_ASM2300632v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:12,484] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:12,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd04f83ad-41f8-402d-93d3-0470cb08bb01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:12,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd04f83ad-41f8-402d-93d3-0470cb08bb01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:12,501] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:12,501] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:12,501] [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
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	100.0	1216	1218	95	conclusive
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	78.4829	402	1218	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	78.464	400	1218	95	below_threshold
Kordiimonas gwangyangensis	strain=DSM 19435	GCA_000375545.1	288022	288022	type	True	78.3666	389	1218	95	below_threshold
Kordiimonas gwangyangensis	strain=JCM 12864	GCA_000616065.1	288022	288022	type	True	78.3388	390	1218	95	below_threshold
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	78.1248	392	1218	95	below_threshold
Eilatimonas milleporae	strain=DSM 25217	GCA_003688555.1	911205	911205	type	True	76.8426	160	1218	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.2591	101	1218	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	76.1699	77	1218	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	76.1602	67	1218	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.1532	89	1218	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	76.1532	78	1218	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	76.0025	89	1218	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	75.9274	58	1218	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	75.9261	58	1218	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.7575	86	1218	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	75.4863	66	1218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:12,503] [INFO] DFAST Taxonomy check result was written to GCF_023006325.1_ASM2300632v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:12,504] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:12,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:12,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd04f83ad-41f8-402d-93d3-0470cb08bb01/dqc_reference/checkm_data
[2024-01-24 14:03:12,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:12,547] [INFO] Task started: CheckM
[2024-01-24 14:03:12,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023006325.1_ASM2300632v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023006325.1_ASM2300632v1_genomic.fna/checkm_input GCF_023006325.1_ASM2300632v1_genomic.fna/checkm_result
[2024-01-24 14:03:48,237] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:48,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:48,257] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:48,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:48,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023006325.1_ASM2300632v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:48,259] [INFO] Task started: Blastn
[2024-01-24 14:03:48,259] [INFO] Running command: blastn -query GCF_023006325.1_ASM2300632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd04f83ad-41f8-402d-93d3-0470cb08bb01/dqc_reference/reference_markers_gtdb.fasta -out GCF_023006325.1_ASM2300632v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:49,742] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:49,746] [INFO] Selected 14 target genomes.
[2024-01-24 14:03:49,746] [INFO] Target genome list was writen to GCF_023006325.1_ASM2300632v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:49,782] [INFO] Task started: fastANI
[2024-01-24 14:03:49,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f6c5b1-29e2-46ec-8208-a88356f124b8/GCF_023006325.1_ASM2300632v1_genomic.fna.gz --refList GCF_023006325.1_ASM2300632v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023006325.1_ASM2300632v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:03:58,451] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:58,463] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:03:58,464] [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
GCA_006226495.1	s__Kordiimonas sp006226495	80.537	673	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550055.1	s__Kordiimonas lacus	78.4741	404	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCF_000375545.1	s__Kordiimonas gwangyangensis	78.3666	389	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	99.96	99.96	1.00	1.00	2	-
GCF_001550065.1	s__Kordiimonas lipolytica	78.1249	392	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372925.1	s__Kordiimonas sp013372925	77.0724	183	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688555.1	s__Eilatimonas milleporae	76.8426	160	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Eilatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640725.1	s__Kordiimonas sp017640725	76.2846	110	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	100.00	100.00	0.99	0.98	3	-
GCA_011088215.1	s__Kordiimonas sp011088215	76.2686	57	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013093415.1	s__Halovulum dunhuangense	76.1532	89	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143235.1	s__Erythrobacter sanguineus	75.9474	59	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_015485385.1	s__Kordiimonas sp015485385	75.9388	70	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	75.8325	63	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100475.1	s__Sphingobium faniae	75.4945	72	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	75.4832	74	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:03:58,466] [INFO] GTDB search result was written to GCF_023006325.1_ASM2300632v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:03:58,466] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:03:58,470] [INFO] DFAST_QC result json was written to GCF_023006325.1_ASM2300632v1_genomic.fna/dqc_result.json
[2024-01-24 14:03:58,471] [INFO] DFAST_QC completed!
[2024-01-24 14:03:58,471] [INFO] Total running time: 0h1m11s