[2024-01-25 20:15:35,472] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:35,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:35,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg34dab3db-eec1-4aea-a332-10b21dd301a7/dqc_reference
[2024-01-25 20:15:36,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:36,662] [INFO] Task started: Prodigal
[2024-01-25 20:15:36,662] [INFO] Running command: gunzip -c /var/lib/cwl/stg15abe75f-4f0e-4d1b-87d5-3f034f5384ca/GCF_024721605.1_ASM2472160v1_genomic.fna.gz | prodigal -d GCF_024721605.1_ASM2472160v1_genomic.fna/cds.fna -a GCF_024721605.1_ASM2472160v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:43,314] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:43,314] [INFO] Task started: HMMsearch
[2024-01-25 20:15:43,314] [INFO] Running command: hmmsearch --tblout GCF_024721605.1_ASM2472160v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34dab3db-eec1-4aea-a332-10b21dd301a7/dqc_reference/reference_markers.hmm GCF_024721605.1_ASM2472160v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:43,506] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:43,507] [INFO] Found 6/6 markers.
[2024-01-25 20:15:43,531] [INFO] Query marker FASTA was written to GCF_024721605.1_ASM2472160v1_genomic.fna/markers.fasta
[2024-01-25 20:15:43,531] [INFO] Task started: Blastn
[2024-01-25 20:15:43,531] [INFO] Running command: blastn -query GCF_024721605.1_ASM2472160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34dab3db-eec1-4aea-a332-10b21dd301a7/dqc_reference/reference_markers.fasta -out GCF_024721605.1_ASM2472160v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:44,349] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:44,353] [INFO] Selected 13 target genomes.
[2024-01-25 20:15:44,353] [INFO] Target genome list was writen to GCF_024721605.1_ASM2472160v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:44,426] [INFO] Task started: fastANI
[2024-01-25 20:15:44,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg15abe75f-4f0e-4d1b-87d5-3f034f5384ca/GCF_024721605.1_ASM2472160v1_genomic.fna.gz --refList GCF_024721605.1_ASM2472160v1_genomic.fna/target_genomes.txt --output GCF_024721605.1_ASM2472160v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:51,156] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:51,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34dab3db-eec1-4aea-a332-10b21dd301a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:51,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34dab3db-eec1-4aea-a332-10b21dd301a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:51,165] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:51,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:51,166] [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
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	100.0	778	779	95	conclusive
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	80.7186	503	779	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	79.5068	454	779	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	79.501	456	779	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	79.3714	422	779	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.1015	281	779	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	78.0536	248	779	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	78.0323	291	779	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	77.8085	249	779	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.5634	233	779	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.2608	157	779	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.1227	202	779	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	76.8947	134	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:51,167] [INFO] DFAST Taxonomy check result was written to GCF_024721605.1_ASM2472160v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:51,168] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:51,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:51,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34dab3db-eec1-4aea-a332-10b21dd301a7/dqc_reference/checkm_data
[2024-01-25 20:15:51,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:51,195] [INFO] Task started: CheckM
[2024-01-25 20:15:51,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024721605.1_ASM2472160v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024721605.1_ASM2472160v1_genomic.fna/checkm_input GCF_024721605.1_ASM2472160v1_genomic.fna/checkm_result
[2024-01-25 20:16:14,816] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:14,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:14,833] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:14,833] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:14,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024721605.1_ASM2472160v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:14,835] [INFO] Task started: Blastn
[2024-01-25 20:16:14,835] [INFO] Running command: blastn -query GCF_024721605.1_ASM2472160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34dab3db-eec1-4aea-a332-10b21dd301a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_024721605.1_ASM2472160v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:16,480] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:16,484] [INFO] Selected 25 target genomes.
[2024-01-25 20:16:16,484] [INFO] Target genome list was writen to GCF_024721605.1_ASM2472160v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:16,507] [INFO] Task started: fastANI
[2024-01-25 20:16:16,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg15abe75f-4f0e-4d1b-87d5-3f034f5384ca/GCF_024721605.1_ASM2472160v1_genomic.fna.gz --refList GCF_024721605.1_ASM2472160v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024721605.1_ASM2472160v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:30,751] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:30,765] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:16:30,766] [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_014195685.1	s__Sphingomicrobium lutaoense	80.731	502	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001055.1	s__Sphingomicrobium sp004282935	79.4205	390	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	99.85	99.85	0.95	0.95	2	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	78.9494	358	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352855.1	s__Sphingomicrobium sp014352855	78.2212	264	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396585.1	s__Sphingomicrobium rhizophilum	78.1015	281	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007998985.1	s__Sphingomicrobium xanthus	78.0536	248	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	78.0289	292	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396785.1	s__Sphingomicrobium lutea	77.9391	254	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011301715.1	s__Sphingomicrobium sp011301715	77.7443	203	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315525.1	s__Sphingobium yanoikuyae	77.7301	263	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	77.6449	221	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	77.5567	195	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	77.5039	184	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111125.1	s__Sphingobium sp900111125	77.4366	225	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797515.1	s__Sphingomonas sp000797515	77.4083	191	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.00	97.12	0.86	0.75	5	-
GCF_000241465.1	s__Sphingomonas echinoides	77.3135	215	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.65	96.65	0.85	0.85	2	-
GCF_013409985.1	s__Sphingomonas melonis_A	77.2634	221	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502465.1	s__Sphingopyxis sp005502465	77.2628	226	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789535.1	s__Sphingomonas carotinifaciens	77.1809	214	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.06	97.19	0.97	0.90	4	-
GCF_001476895.1	s__Sphingomonas endophytica_A	77.0341	182	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653575.1	s__Sphingomonas glacialis	77.0289	201	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCF_001634625.1	s__Croceicoccus bisphenolivorans	77.0137	149	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239785.1	s__Allosphingosinicella sp019239785	76.4871	166	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911985.1	s__Novosphingobium sp903911985	76.0144	88	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:30,767] [INFO] GTDB search result was written to GCF_024721605.1_ASM2472160v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:30,767] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:30,771] [INFO] DFAST_QC result json was written to GCF_024721605.1_ASM2472160v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:30,771] [INFO] DFAST_QC completed!
[2024-01-25 20:16:30,771] [INFO] Total running time: 0h0m55s