[2024-01-24 14:11:46,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c6791ea-b16b-47f9-9f5f-ffd3d16a57c2/dqc_reference
[2024-01-24 14:11:48,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:48,879] [INFO] Task started: Prodigal
[2024-01-24 14:11:48,879] [INFO] Running command: gunzip -c /var/lib/cwl/stga695a7c0-314d-48b1-bde8-54003c1394e3/GCF_023516455.1_ASM2351645v1_genomic.fna.gz | prodigal -d GCF_023516455.1_ASM2351645v1_genomic.fna/cds.fna -a GCF_023516455.1_ASM2351645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:11:57,332] [INFO] Task succeeded: Prodigal
[2024-01-24 14:11:57,332] [INFO] Task started: HMMsearch
[2024-01-24 14:11:57,332] [INFO] Running command: hmmsearch --tblout GCF_023516455.1_ASM2351645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c6791ea-b16b-47f9-9f5f-ffd3d16a57c2/dqc_reference/reference_markers.hmm GCF_023516455.1_ASM2351645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:11:57,636] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:11:57,637] [INFO] Found 6/6 markers.
[2024-01-24 14:11:57,674] [INFO] Query marker FASTA was written to GCF_023516455.1_ASM2351645v1_genomic.fna/markers.fasta
[2024-01-24 14:11:57,675] [INFO] Task started: Blastn
[2024-01-24 14:11:57,675] [INFO] Running command: blastn -query GCF_023516455.1_ASM2351645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c6791ea-b16b-47f9-9f5f-ffd3d16a57c2/dqc_reference/reference_markers.fasta -out GCF_023516455.1_ASM2351645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:58,908] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:58,911] [INFO] Selected 20 target genomes.
[2024-01-24 14:11:58,911] [INFO] Target genome list was writen to GCF_023516455.1_ASM2351645v1_genomic.fna/target_genomes.txt
[2024-01-24 14:11:58,920] [INFO] Task started: fastANI
[2024-01-24 14:11:58,921] [INFO] Running command: fastANI --query /var/lib/cwl/stga695a7c0-314d-48b1-bde8-54003c1394e3/GCF_023516455.1_ASM2351645v1_genomic.fna.gz --refList GCF_023516455.1_ASM2351645v1_genomic.fna/target_genomes.txt --output GCF_023516455.1_ASM2351645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:11,337] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:11,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c6791ea-b16b-47f9-9f5f-ffd3d16a57c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:11,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c6791ea-b16b-47f9-9f5f-ffd3d16a57c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:11,427] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:12:11,428] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:12:11,428] [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	79.9328	417	924	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	79.4826	420	924	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.4796	384	924	95	below_threshold
Sphingomonas edaphi	strain=DAC4	GCA_003583725.1	2315689	2315689	type	True	79.3788	366	924	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.2077	342	924	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	78.9378	291	924	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	78.8811	319	924	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.8722	323	924	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.8509	331	924	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	78.8113	333	924	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	78.7992	332	924	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.7294	249	924	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	78.5152	292	924	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	78.0924	264	924	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	77.9025	212	924	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.8358	191	924	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.83	197	924	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	77.6866	224	924	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.573	270	924	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.5568	198	924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:11,439] [INFO] DFAST Taxonomy check result was written to GCF_023516455.1_ASM2351645v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:11,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:11,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:11,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c6791ea-b16b-47f9-9f5f-ffd3d16a57c2/dqc_reference/checkm_data
[2024-01-24 14:12:11,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:11,504] [INFO] Task started: CheckM
[2024-01-24 14:12:11,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023516455.1_ASM2351645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023516455.1_ASM2351645v1_genomic.fna/checkm_input GCF_023516455.1_ASM2351645v1_genomic.fna/checkm_result
[2024-01-24 14:12:41,777] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:41,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:41,801] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:41,801] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:41,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023516455.1_ASM2351645v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:41,802] [INFO] Task started: Blastn
[2024-01-24 14:12:41,802] [INFO] Running command: blastn -query GCF_023516455.1_ASM2351645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c6791ea-b16b-47f9-9f5f-ffd3d16a57c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_023516455.1_ASM2351645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:45,399] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:45,403] [INFO] Selected 21 target genomes.
[2024-01-24 14:12:45,404] [INFO] Target genome list was writen to GCF_023516455.1_ASM2351645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:45,426] [INFO] Task started: fastANI
[2024-01-24 14:12:45,426] [INFO] Running command: fastANI --query /var/lib/cwl/stga695a7c0-314d-48b1-bde8-54003c1394e3/GCF_023516455.1_ASM2351645v1_genomic.fna.gz --refList GCF_023516455.1_ASM2351645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023516455.1_ASM2351645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:58,006] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:58,037] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:12:58,037] [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_000585415.1	s__Sphingomicrobium jaspsi	79.9202	418	924	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	79.4863	383	924	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	79.4826	420	924	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	79.378	366	924	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	79.3132	308	924	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	79.1938	343	924	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	78.9602	289	924	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	78.921	348	924	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	78.892	321	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014352855.1	s__Sphingomicrobium sp014352855	78.89	310	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	78.8509	331	924	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	78.7992	332	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873375.1	s__Sphingomicrobium sp014873375	78.7758	265	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873475.1	s__Sphingomicrobium sp014873475	78.7725	322	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242355.1	s__Sphingomicrobium sp019242355	78.5291	225	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924655.1	s__Sphingomicrobium sp016924655	78.4949	293	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003347635.1	s__Allosphingosinicella sp003347635	78.1813	249	924	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	78.0349	248	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197035.1	s__Sphingobium scionense	77.8873	213	924	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	77.7856	173	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.00	97.12	0.86	0.75	5	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	77.6301	199	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:12:58,039] [INFO] GTDB search result was written to GCF_023516455.1_ASM2351645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:58,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:58,045] [INFO] DFAST_QC result json was written to GCF_023516455.1_ASM2351645v1_genomic.fna/dqc_result.json
[2024-01-24 14:12:58,045] [INFO] DFAST_QC completed!
[2024-01-24 14:12:58,045] [INFO] Total running time: 0h1m12s