[2024-01-25 20:22:05,602] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:05,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:05,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg461a3ea4-3d11-43f0-8a38-6544bb3c6920/dqc_reference
[2024-01-25 20:22:06,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:06,765] [INFO] Task started: Prodigal
[2024-01-25 20:22:06,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg987ba93b-4ef0-4122-97d2-2af7b27b80bb/GCF_009363895.1_ASM936389v1_genomic.fna.gz | prodigal -d GCF_009363895.1_ASM936389v1_genomic.fna/cds.fna -a GCF_009363895.1_ASM936389v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:14,566] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:14,567] [INFO] Task started: HMMsearch
[2024-01-25 20:22:14,567] [INFO] Running command: hmmsearch --tblout GCF_009363895.1_ASM936389v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg461a3ea4-3d11-43f0-8a38-6544bb3c6920/dqc_reference/reference_markers.hmm GCF_009363895.1_ASM936389v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:14,786] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:14,787] [INFO] Found 6/6 markers.
[2024-01-25 20:22:14,814] [INFO] Query marker FASTA was written to GCF_009363895.1_ASM936389v1_genomic.fna/markers.fasta
[2024-01-25 20:22:14,814] [INFO] Task started: Blastn
[2024-01-25 20:22:14,814] [INFO] Running command: blastn -query GCF_009363895.1_ASM936389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg461a3ea4-3d11-43f0-8a38-6544bb3c6920/dqc_reference/reference_markers.fasta -out GCF_009363895.1_ASM936389v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:15,802] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:15,806] [INFO] Selected 14 target genomes.
[2024-01-25 20:22:15,806] [INFO] Target genome list was writen to GCF_009363895.1_ASM936389v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:15,818] [INFO] Task started: fastANI
[2024-01-25 20:22:15,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg987ba93b-4ef0-4122-97d2-2af7b27b80bb/GCF_009363895.1_ASM936389v1_genomic.fna.gz --refList GCF_009363895.1_ASM936389v1_genomic.fna/target_genomes.txt --output GCF_009363895.1_ASM936389v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:25,161] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:25,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg461a3ea4-3d11-43f0-8a38-6544bb3c6920/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:25,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg461a3ea4-3d11-43f0-8a38-6544bb3c6920/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:25,171] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:22:25,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:25,172] [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 ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	100.0	1012	1012	95	conclusive
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	81.9239	574	1012	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	81.0854	517	1012	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	80.6971	533	1012	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	80.2759	427	1012	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	80.0204	435	1012	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.6234	414	1012	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	79.4479	339	1012	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	79.4029	385	1012	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.328	391	1012	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	78.488	320	1012	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.3975	390	1012	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.3697	417	1012	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.9831	304	1012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:25,173] [INFO] DFAST Taxonomy check result was written to GCF_009363895.1_ASM936389v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:25,173] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:25,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:25,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg461a3ea4-3d11-43f0-8a38-6544bb3c6920/dqc_reference/checkm_data
[2024-01-25 20:22:25,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:25,205] [INFO] Task started: CheckM
[2024-01-25 20:22:25,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009363895.1_ASM936389v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009363895.1_ASM936389v1_genomic.fna/checkm_input GCF_009363895.1_ASM936389v1_genomic.fna/checkm_result
[2024-01-25 20:22:50,736] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:50,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:50,754] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:50,755] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:50,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009363895.1_ASM936389v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:50,755] [INFO] Task started: Blastn
[2024-01-25 20:22:50,755] [INFO] Running command: blastn -query GCF_009363895.1_ASM936389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg461a3ea4-3d11-43f0-8a38-6544bb3c6920/dqc_reference/reference_markers_gtdb.fasta -out GCF_009363895.1_ASM936389v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:52,684] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:52,688] [INFO] Selected 12 target genomes.
[2024-01-25 20:22:52,688] [INFO] Target genome list was writen to GCF_009363895.1_ASM936389v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:52,700] [INFO] Task started: fastANI
[2024-01-25 20:22:52,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg987ba93b-4ef0-4122-97d2-2af7b27b80bb/GCF_009363895.1_ASM936389v1_genomic.fna.gz --refList GCF_009363895.1_ASM936389v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009363895.1_ASM936389v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:59,669] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:59,678] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:59,678] [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_009363895.1	s__Sphingomicrobium ginsengisoli	100.0	1012	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000711715.1	s__Sphingomicrobium astaxanthinifaciens	81.957	572	1012	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	81.0722	518	1012	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	80.722	531	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	80.323	443	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806265.1	s__Sphingomicrobium sp902806265	80.0003	451	1012	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	79.9956	437	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	79.9409	332	1012	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	79.6431	412	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720245.1	s__Sphingomicrobium sp009720245	79.4914	336	1012	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	79.4787	396	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014396585.1	s__Sphingomicrobium rhizophilum	79.3902	385	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:59,679] [INFO] GTDB search result was written to GCF_009363895.1_ASM936389v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:59,680] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:59,683] [INFO] DFAST_QC result json was written to GCF_009363895.1_ASM936389v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:59,683] [INFO] DFAST_QC completed!
[2024-01-25 20:22:59,683] [INFO] Total running time: 0h0m54s