[2024-01-24 15:17:49,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:49,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:49,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb997266-5672-4965-b7cc-946425f803cc/dqc_reference
[2024-01-24 15:17:51,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,534] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg919af0fd-3fa3-4a9c-935a-8457c732f080/GCF_003660165.1_ASM366016v1_genomic.fna.gz | prodigal -d GCF_003660165.1_ASM366016v1_genomic.fna/cds.fna -a GCF_003660165.1_ASM366016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:03,579] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:03,579] [INFO] Task started: HMMsearch
[2024-01-24 15:18:03,580] [INFO] Running command: hmmsearch --tblout GCF_003660165.1_ASM366016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb997266-5672-4965-b7cc-946425f803cc/dqc_reference/reference_markers.hmm GCF_003660165.1_ASM366016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:03,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:03,869] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg919af0fd-3fa3-4a9c-935a-8457c732f080/GCF_003660165.1_ASM366016v1_genomic.fna.gz]
[2024-01-24 15:18:03,908] [INFO] Query marker FASTA was written to GCF_003660165.1_ASM366016v1_genomic.fna/markers.fasta
[2024-01-24 15:18:03,908] [INFO] Task started: Blastn
[2024-01-24 15:18:03,909] [INFO] Running command: blastn -query GCF_003660165.1_ASM366016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb997266-5672-4965-b7cc-946425f803cc/dqc_reference/reference_markers.fasta -out GCF_003660165.1_ASM366016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:04,686] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:04,689] [INFO] Selected 24 target genomes.
[2024-01-24 15:18:04,690] [INFO] Target genome list was writen to GCF_003660165.1_ASM366016v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:04,699] [INFO] Task started: fastANI
[2024-01-24 15:18:04,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg919af0fd-3fa3-4a9c-935a-8457c732f080/GCF_003660165.1_ASM366016v1_genomic.fna.gz --refList GCF_003660165.1_ASM366016v1_genomic.fna/target_genomes.txt --output GCF_003660165.1_ASM366016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:21,916] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:21,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb997266-5672-4965-b7cc-946425f803cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:21,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb997266-5672-4965-b7cc-946425f803cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:21,935] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:21,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:21,935] [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 paeninsulae	strain=YZ-8	GCA_003660165.1	2319844	2319844	type	True	100.0	1329	1330	95	conclusive
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.4472	204	1330	95	below_threshold
Sphingobium boeckii	strain=DSM 25079	GCA_014199215.1	1082345	1082345	type	True	77.3022	193	1330	95	below_threshold
Sphingomonas aliaeris	strain=DH-S5	GCA_016743815.1	2759526	2759526	type	True	77.2366	190	1330	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	77.196	174	1330	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.1918	186	1330	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.1889	213	1330	95	below_threshold
Sphingomonas faeni	strain=MA-olki	GCA_003053745.1	185950	185950	type	True	77.0821	194	1330	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.048	166	1330	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.0459	197	1330	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.0356	168	1330	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	77.0323	159	1330	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	77.022	160	1330	95	below_threshold
Aquisediminimonas profunda	strain=DS48-3	GCA_019443285.1	1550733	1550733	type	True	77.0027	97	1330	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.9659	103	1330	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	76.9562	82	1330	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	76.9543	189	1330	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	76.9412	181	1330	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	76.9249	83	1330	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	76.91	160	1330	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.7663	162	1330	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	76.7346	171	1330	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	76.6579	166	1330	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	76.1226	132	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:21,937] [INFO] DFAST Taxonomy check result was written to GCF_003660165.1_ASM366016v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:21,937] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:21,937] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:21,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb997266-5672-4965-b7cc-946425f803cc/dqc_reference/checkm_data
[2024-01-24 15:18:21,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:21,981] [INFO] Task started: CheckM
[2024-01-24 15:18:21,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003660165.1_ASM366016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003660165.1_ASM366016v1_genomic.fna/checkm_input GCF_003660165.1_ASM366016v1_genomic.fna/checkm_result
[2024-01-24 15:19:00,526] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:00,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:00,548] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:00,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:00,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003660165.1_ASM366016v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:00,549] [INFO] Task started: Blastn
[2024-01-24 15:19:00,549] [INFO] Running command: blastn -query GCF_003660165.1_ASM366016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb997266-5672-4965-b7cc-946425f803cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003660165.1_ASM366016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:01,887] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:01,892] [INFO] Selected 21 target genomes.
[2024-01-24 15:19:01,893] [INFO] Target genome list was writen to GCF_003660165.1_ASM366016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:01,939] [INFO] Task started: fastANI
[2024-01-24 15:19:01,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg919af0fd-3fa3-4a9c-935a-8457c732f080/GCF_003660165.1_ASM366016v1_genomic.fna.gz --refList GCF_003660165.1_ASM366016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003660165.1_ASM366016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:16,862] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:16,887] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:16,887] [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_003660165.1	s__UBA1936 sp003660165	100.0	1329	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA1936	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002336985.1	s__UBA1936 sp002336985	77.517	190	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA1936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821585.1	s__UBA1936 sp013821585	77.3449	169	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA1936	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199215.1	s__Sphingobium_A boeckii	77.288	194	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050745.1	s__Sphingomonas sp003050745	77.1788	189	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.19	95.12	0.89	0.88	3	-
GCF_000786205.1	s__Sphingomonas sp000786205	77.17	169	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	77.1672	195	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_004341085.1	s__Sphingomonas sp004341085	77.1562	190	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590775.1	s__Sphingobium_A sp003590775	77.1463	187	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744515.1	s__Rhizorhabdus wittichii_A	77.0857	185	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	77.0422	211	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005865.1	s__Rhizorhabdus crocodyli	77.029	179	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	77.0208	169	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101455.1	s__Rhizorhabdus sp900101455	77.0153	156	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704425.1	s__Chakrabartia sp016704425	76.9577	111	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	98.81	97.63	0.91	0.86	10	-
GCF_012927105.1	s__Sphingobium psychrophilum	76.954	188	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240625.1	s__Sphingomonas taxi_A	76.9335	168	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340945.1	s__Sphingomonas sp004340945	76.8642	191	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
GCA_001724715.1	s__SCN-67-18 sp001724715	76.6862	165	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	76.6635	166	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	76.6579	166	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:16,889] [INFO] GTDB search result was written to GCF_003660165.1_ASM366016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:16,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:16,894] [INFO] DFAST_QC result json was written to GCF_003660165.1_ASM366016v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:16,895] [INFO] DFAST_QC completed!
[2024-01-24 15:19:16,895] [INFO] Total running time: 0h1m27s