[2024-01-24 15:17:49,605] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:49,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:49,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg272922fd-aa1b-4f4b-a9ed-c4f2c2473fd1/dqc_reference
[2024-01-24 15:17:51,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,533] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,534] [INFO] Running command: gunzip -c /var/lib/cwl/stgf43815e3-a081-46ae-95e7-ebbdd4b701a3/GCF_005144965.1_ASM514496v1_genomic.fna.gz | prodigal -d GCF_005144965.1_ASM514496v1_genomic.fna/cds.fna -a GCF_005144965.1_ASM514496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:00,246] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:00,247] [INFO] Task started: HMMsearch
[2024-01-24 15:18:00,247] [INFO] Running command: hmmsearch --tblout GCF_005144965.1_ASM514496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg272922fd-aa1b-4f4b-a9ed-c4f2c2473fd1/dqc_reference/reference_markers.hmm GCF_005144965.1_ASM514496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:00,499] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:00,500] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf43815e3-a081-46ae-95e7-ebbdd4b701a3/GCF_005144965.1_ASM514496v1_genomic.fna.gz]
[2024-01-24 15:18:00,537] [INFO] Query marker FASTA was written to GCF_005144965.1_ASM514496v1_genomic.fna/markers.fasta
[2024-01-24 15:18:00,537] [INFO] Task started: Blastn
[2024-01-24 15:18:00,537] [INFO] Running command: blastn -query GCF_005144965.1_ASM514496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg272922fd-aa1b-4f4b-a9ed-c4f2c2473fd1/dqc_reference/reference_markers.fasta -out GCF_005144965.1_ASM514496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:01,457] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:01,462] [INFO] Selected 25 target genomes.
[2024-01-24 15:18:01,463] [INFO] Target genome list was writen to GCF_005144965.1_ASM514496v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:01,476] [INFO] Task started: fastANI
[2024-01-24 15:18:01,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgf43815e3-a081-46ae-95e7-ebbdd4b701a3/GCF_005144965.1_ASM514496v1_genomic.fna.gz --refList GCF_005144965.1_ASM514496v1_genomic.fna/target_genomes.txt --output GCF_005144965.1_ASM514496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:20,957] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:20,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg272922fd-aa1b-4f4b-a9ed-c4f2c2473fd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:20,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg272922fd-aa1b-4f4b-a9ed-c4f2c2473fd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:20,981] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:20,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:20,982] [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
Hankyongella ginsenosidimutans	strain=W1-2-3	GCA_005144965.1	1763828	1763828	type	True	100.0	958	960	95	conclusive
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	78.2989	247	960	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	77.4764	189	960	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	77.4706	152	960	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	77.3861	192	960	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	77.3676	146	960	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.2823	231	960	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	77.2444	152	960	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.2138	235	960	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	77.1995	131	960	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	77.1553	184	960	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	77.1282	170	960	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	77.1258	83	960	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	77.125	175	960	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	77.1204	184	960	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.0837	166	960	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	77.0608	192	960	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.0124	135	960	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.9127	165	960	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.8189	156	960	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.8186	147	960	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.7136	220	960	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.5552	137	960	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5541	106	960	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.4276	197	960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:20,983] [INFO] DFAST Taxonomy check result was written to GCF_005144965.1_ASM514496v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:20,984] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:20,984] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:20,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg272922fd-aa1b-4f4b-a9ed-c4f2c2473fd1/dqc_reference/checkm_data
[2024-01-24 15:18:20,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:21,016] [INFO] Task started: CheckM
[2024-01-24 15:18:21,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005144965.1_ASM514496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005144965.1_ASM514496v1_genomic.fna/checkm_input GCF_005144965.1_ASM514496v1_genomic.fna/checkm_result
[2024-01-24 15:18:51,620] [INFO] Task succeeded: CheckM
[2024-01-24 15:18:51,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:18:51,643] [INFO] ===== Completeness check finished =====
[2024-01-24 15:18:51,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:18:51,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005144965.1_ASM514496v1_genomic.fna/markers.fasta)
[2024-01-24 15:18:51,644] [INFO] Task started: Blastn
[2024-01-24 15:18:51,645] [INFO] Running command: blastn -query GCF_005144965.1_ASM514496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg272922fd-aa1b-4f4b-a9ed-c4f2c2473fd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_005144965.1_ASM514496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:53,353] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:53,358] [INFO] Selected 25 target genomes.
[2024-01-24 15:18:53,358] [INFO] Target genome list was writen to GCF_005144965.1_ASM514496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:18:53,382] [INFO] Task started: fastANI
[2024-01-24 15:18:53,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgf43815e3-a081-46ae-95e7-ebbdd4b701a3/GCF_005144965.1_ASM514496v1_genomic.fna.gz --refList GCF_005144965.1_ASM514496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005144965.1_ASM514496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:11,392] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:11,411] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:11,412] [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
GCA_005144965.1	s__Hankyongella ginsenosidimutans	100.0	959	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Hankyongella	95.0	98.05	98.05	0.80	0.80	2	conclusive
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	77.5273	176	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	77.4901	151	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464365.1	s__Sandaracinobacter sp016464365	77.4686	148	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778325.1	s__Sphingomonas_N chungangi	77.3864	192	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	77.3239	208	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018006725.1	s__Rhizorhabdus sp018006725	77.3147	177	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	77.2805	178	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097155.1	s__Glacieibacterium frigidum	77.2289	210	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	77.2157	200	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643455.1	s__Polymorphobacter glacialis	77.1995	131	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	77.176	189	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	77.0281	179	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCF_014117445.1	s__GCA-014117445 sp014117445	77.0208	180	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__GCA-014117445	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100155.1	s__Ancylobacter rudongensis	77.0124	135	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCF_000419605.1	s__Sphingomonas phyllosphaerae_B	76.9969	156	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793845.1	s__Sphingosinicella sp016793845	76.9891	171	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241875.1	s__Polymorphobacter sp003241875	76.9774	196	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	76.9127	165	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243195.1	s__Sphingomonas taxi_B	76.8021	200	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421535.1	s__Sphingomonas sp001421535	76.7783	152	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	76.7575	141	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349105.1	s__17J80-11 sp014349105	76.5974	170	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467395.1	s__Reyranella sp016467395	76.5809	157	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	76.5457	143	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:11,413] [INFO] GTDB search result was written to GCF_005144965.1_ASM514496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:11,414] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:11,419] [INFO] DFAST_QC result json was written to GCF_005144965.1_ASM514496v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:11,419] [INFO] DFAST_QC completed!
[2024-01-24 15:19:11,419] [INFO] Total running time: 0h1m22s