[2024-01-24 12:23:04,001] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:04,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:04,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg0627cc85-8673-4483-bac6-0fbdc3d23bd7/dqc_reference
[2024-01-24 12:23:05,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,278] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7b5d673-b9c1-4134-b07e-089e5e741819/GCF_021502585.1_ASM2150258v1_genomic.fna.gz | prodigal -d GCF_021502585.1_ASM2150258v1_genomic.fna/cds.fna -a GCF_021502585.1_ASM2150258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:13,288] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:13,289] [INFO] Task started: HMMsearch
[2024-01-24 12:23:13,289] [INFO] Running command: hmmsearch --tblout GCF_021502585.1_ASM2150258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0627cc85-8673-4483-bac6-0fbdc3d23bd7/dqc_reference/reference_markers.hmm GCF_021502585.1_ASM2150258v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:13,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:13,553] [INFO] Found 6/6 markers.
[2024-01-24 12:23:13,585] [INFO] Query marker FASTA was written to GCF_021502585.1_ASM2150258v1_genomic.fna/markers.fasta
[2024-01-24 12:23:13,585] [INFO] Task started: Blastn
[2024-01-24 12:23:13,586] [INFO] Running command: blastn -query GCF_021502585.1_ASM2150258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0627cc85-8673-4483-bac6-0fbdc3d23bd7/dqc_reference/reference_markers.fasta -out GCF_021502585.1_ASM2150258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:14,499] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:14,503] [INFO] Selected 18 target genomes.
[2024-01-24 12:23:14,503] [INFO] Target genome list was writen to GCF_021502585.1_ASM2150258v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:14,511] [INFO] Task started: fastANI
[2024-01-24 12:23:14,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7b5d673-b9c1-4134-b07e-089e5e741819/GCF_021502585.1_ASM2150258v1_genomic.fna.gz --refList GCF_021502585.1_ASM2150258v1_genomic.fna/target_genomes.txt --output GCF_021502585.1_ASM2150258v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:23,752] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:23,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0627cc85-8673-4483-bac6-0fbdc3d23bd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:23,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0627cc85-8673-4483-bac6-0fbdc3d23bd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:23,769] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:23,769] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:23,770] [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
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.4023	403	846	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	79.3909	366	846	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.343	343	846	95	below_threshold
Sphingomonas edaphi	strain=DAC4	GCA_003583725.1	2315689	2315689	type	True	79.1702	349	846	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.1209	320	846	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.9169	295	846	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.728	307	846	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	78.6544	297	846	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	78.631	256	846	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.5873	240	846	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	78.4603	288	846	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	78.3244	233	846	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	77.722	191	846	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.5254	201	846	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	77.3846	187	846	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.3675	176	846	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	76.1089	54	846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:23,771] [INFO] DFAST Taxonomy check result was written to GCF_021502585.1_ASM2150258v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:23,772] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:23,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:23,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0627cc85-8673-4483-bac6-0fbdc3d23bd7/dqc_reference/checkm_data
[2024-01-24 12:23:23,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:23,802] [INFO] Task started: CheckM
[2024-01-24 12:23:23,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021502585.1_ASM2150258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021502585.1_ASM2150258v1_genomic.fna/checkm_input GCF_021502585.1_ASM2150258v1_genomic.fna/checkm_result
[2024-01-24 12:23:50,848] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:50,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:50,875] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:50,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:50,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021502585.1_ASM2150258v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:50,877] [INFO] Task started: Blastn
[2024-01-24 12:23:50,877] [INFO] Running command: blastn -query GCF_021502585.1_ASM2150258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0627cc85-8673-4483-bac6-0fbdc3d23bd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_021502585.1_ASM2150258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:52,496] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:52,501] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:52,502] [INFO] Target genome list was writen to GCF_021502585.1_ASM2150258v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:52,513] [INFO] Task started: fastANI
[2024-01-24 12:23:52,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7b5d673-b9c1-4134-b07e-089e5e741819/GCF_021502585.1_ASM2150258v1_genomic.fna.gz --refList GCF_021502585.1_ASM2150258v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021502585.1_ASM2150258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:00,215] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:00,236] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:00,236] [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_007998985.1	s__Sphingomicrobium xanthus	79.3909	366	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	79.3779	405	846	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	79.3422	343	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	79.2867	293	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816785.1	s__Sphingomicrobium sp013816785	79.2251	369	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583725.1	s__Sphingomicrobium edaphi	79.1702	349	846	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	79.1131	320	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363895.1	s__Sphingomicrobium ginsengisoli	78.9322	294	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	78.728	307	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302055.1	s__Sphingomicrobium sinipercae	78.631	256	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927725.1	s__Sphingomicrobium kaistense	78.474	287	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320075.1	s__Allosphingosinicella sp011320075	78.2817	229	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883305.1	s__Allosphingosinicella sp005883305	78.0024	214	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598435.1	s__Sphingomonas pituitosa	77.722	191	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001055.1	s__Sphingomicrobium sp004282935	77.2311	164	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	99.85	99.85	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,239] [INFO] GTDB search result was written to GCF_021502585.1_ASM2150258v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:00,240] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:00,247] [INFO] DFAST_QC result json was written to GCF_021502585.1_ASM2150258v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:00,247] [INFO] DFAST_QC completed!
[2024-01-24 12:24:00,248] [INFO] Total running time: 0h0m56s