[2024-01-25 20:16:35,601] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:35,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:35,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c0e74eb-c692-4a3f-b284-c913a4a05c3e/dqc_reference
[2024-01-25 20:16:36,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:36,784] [INFO] Task started: Prodigal
[2024-01-25 20:16:36,785] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3802f75-dcdb-40c5-9671-be8caf211169/GCF_024721585.1_ASM2472158v1_genomic.fna.gz | prodigal -d GCF_024721585.1_ASM2472158v1_genomic.fna/cds.fna -a GCF_024721585.1_ASM2472158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:43,067] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:43,067] [INFO] Task started: HMMsearch
[2024-01-25 20:16:43,068] [INFO] Running command: hmmsearch --tblout GCF_024721585.1_ASM2472158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c0e74eb-c692-4a3f-b284-c913a4a05c3e/dqc_reference/reference_markers.hmm GCF_024721585.1_ASM2472158v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:43,256] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:43,257] [INFO] Found 6/6 markers.
[2024-01-25 20:16:43,278] [INFO] Query marker FASTA was written to GCF_024721585.1_ASM2472158v1_genomic.fna/markers.fasta
[2024-01-25 20:16:43,278] [INFO] Task started: Blastn
[2024-01-25 20:16:43,278] [INFO] Running command: blastn -query GCF_024721585.1_ASM2472158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0e74eb-c692-4a3f-b284-c913a4a05c3e/dqc_reference/reference_markers.fasta -out GCF_024721585.1_ASM2472158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:44,253] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:44,257] [INFO] Selected 13 target genomes.
[2024-01-25 20:16:44,257] [INFO] Target genome list was writen to GCF_024721585.1_ASM2472158v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:44,262] [INFO] Task started: fastANI
[2024-01-25 20:16:44,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3802f75-dcdb-40c5-9671-be8caf211169/GCF_024721585.1_ASM2472158v1_genomic.fna.gz --refList GCF_024721585.1_ASM2472158v1_genomic.fna/target_genomes.txt --output GCF_024721585.1_ASM2472158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:52,476] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:52,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c0e74eb-c692-4a3f-b284-c913a4a05c3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:52,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c0e74eb-c692-4a3f-b284-c913a4a05c3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:52,485] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:16:52,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:52,486] [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 aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	99.9999	782	782	95	conclusive
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	99.9961	779	782	95	conclusive
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	86.4235	623	782	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	80.2968	442	782	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	79.584	433	782	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.9523	366	782	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	78.7751	347	782	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.6349	345	782	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.3877	244	782	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	78.303	294	782	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	78.2811	300	782	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.1559	290	782	95	below_threshold
Sphingomonas lenta	strain=1PNM-20	GCA_002288825.1	1141887	1141887	type	True	77.6706	248	782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:52,487] [INFO] DFAST Taxonomy check result was written to GCF_024721585.1_ASM2472158v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:52,488] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:52,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:52,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c0e74eb-c692-4a3f-b284-c913a4a05c3e/dqc_reference/checkm_data
[2024-01-25 20:16:52,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:52,515] [INFO] Task started: CheckM
[2024-01-25 20:16:52,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024721585.1_ASM2472158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024721585.1_ASM2472158v1_genomic.fna/checkm_input GCF_024721585.1_ASM2472158v1_genomic.fna/checkm_result
[2024-01-25 20:17:15,231] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:15,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:15,253] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:15,253] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:15,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024721585.1_ASM2472158v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:15,253] [INFO] Task started: Blastn
[2024-01-25 20:17:15,253] [INFO] Running command: blastn -query GCF_024721585.1_ASM2472158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0e74eb-c692-4a3f-b284-c913a4a05c3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024721585.1_ASM2472158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:17,199] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:17,202] [INFO] Selected 24 target genomes.
[2024-01-25 20:17:17,202] [INFO] Target genome list was writen to GCF_024721585.1_ASM2472158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:17,220] [INFO] Task started: fastANI
[2024-01-25 20:17:17,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3802f75-dcdb-40c5-9671-be8caf211169/GCF_024721585.1_ASM2472158v1_genomic.fna.gz --refList GCF_024721585.1_ASM2472158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024721585.1_ASM2472158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:35,087] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:35,102] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:17:35,103] [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	80.3062	442	782	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	79.2207	358	782	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	78.9645	365	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003499275.1	s__Sphingomicrobium mesophila	78.7996	345	782	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	78.7926	355	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	99.85	99.85	0.95	0.95	2	-
GCF_011320075.1	s__Allosphingosinicella sp011320075	78.6946	295	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	78.6404	344	782	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	78.3729	245	782	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	78.3034	257	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	78.2558	302	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097155.1	s__Sphingomicrobium sp003097155	78.2368	280	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	78.1912	297	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	78.1685	251	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489495.1	s__Sphingomicrobium daechungense	78.1258	215	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	78.0922	306	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429065.1	s__Rhizorhabdus sp001429065	78.0858	266	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	78.0816	305	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	77.9969	248	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	77.9178	267	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408095.1	s__Novosphingobium marinum	77.9017	196	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004135585.1	s__Allosphingosinicella sp004135585	77.894	265	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	77.851	243	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000803645.1	s__Sphingopyxis fribergensis	77.6963	258	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288825.1	s__Sphingomonas lenta	77.6832	247	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:35,105] [INFO] GTDB search result was written to GCF_024721585.1_ASM2472158v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:35,106] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:35,110] [INFO] DFAST_QC result json was written to GCF_024721585.1_ASM2472158v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:35,111] [INFO] DFAST_QC completed!
[2024-01-25 20:17:35,111] [INFO] Total running time: 0h0m60s