[2024-01-24 14:31:00,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg83743938-5c56-4543-bc2a-1c5d977d2081/dqc_reference
[2024-01-24 14:31:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,103] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg0966c40a-7a0d-49e4-a6d0-907ac15d94e5/GCF_004005485.1_ASM400548v1_genomic.fna.gz | prodigal -d GCF_004005485.1_ASM400548v1_genomic.fna/cds.fna -a GCF_004005485.1_ASM400548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:12,960] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:12,960] [INFO] Task started: HMMsearch
[2024-01-24 14:31:12,960] [INFO] Running command: hmmsearch --tblout GCF_004005485.1_ASM400548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83743938-5c56-4543-bc2a-1c5d977d2081/dqc_reference/reference_markers.hmm GCF_004005485.1_ASM400548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:13,307] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:13,316] [INFO] Found 6/6 markers.
[2024-01-24 14:31:13,345] [INFO] Query marker FASTA was written to GCF_004005485.1_ASM400548v1_genomic.fna/markers.fasta
[2024-01-24 14:31:13,345] [INFO] Task started: Blastn
[2024-01-24 14:31:13,345] [INFO] Running command: blastn -query GCF_004005485.1_ASM400548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83743938-5c56-4543-bc2a-1c5d977d2081/dqc_reference/reference_markers.fasta -out GCF_004005485.1_ASM400548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:14,318] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:14,320] [INFO] Selected 27 target genomes.
[2024-01-24 14:31:14,321] [INFO] Target genome list was writen to GCF_004005485.1_ASM400548v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:14,329] [INFO] Task started: fastANI
[2024-01-24 14:31:14,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg0966c40a-7a0d-49e4-a6d0-907ac15d94e5/GCF_004005485.1_ASM400548v1_genomic.fna.gz --refList GCF_004005485.1_ASM400548v1_genomic.fna/target_genomes.txt --output GCF_004005485.1_ASM400548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:35,416] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:35,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83743938-5c56-4543-bc2a-1c5d977d2081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:35,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83743938-5c56-4543-bc2a-1c5d977d2081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:35,432] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:35,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:35,432] [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
Sphingobium algorifonticola	strain=TLA-22	GCA_004005485.1	2008318	2008318	type	True	100.0	1257	1262	95	conclusive
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	79.9359	472	1262	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	79.7328	485	1262	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	79.6931	501	1262	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	79.6575	445	1262	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	79.6031	455	1262	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	79.5913	469	1262	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	79.5728	435	1262	95	below_threshold
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	79.5427	439	1262	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	79.5093	446	1262	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	79.4785	507	1262	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	79.4351	473	1262	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	79.4346	461	1262	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	79.3846	458	1262	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	79.2258	500	1262	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	79.2013	407	1262	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	79.1266	490	1262	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	79.0598	475	1262	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	78.4416	365	1262	95	below_threshold
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	78.0485	336	1262	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	78.0313	304	1262	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	77.6854	285	1262	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.6663	315	1262	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	77.6662	292	1262	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.5019	288	1262	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	77.3966	300	1262	95	below_threshold
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	77.2563	235	1262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,434] [INFO] DFAST Taxonomy check result was written to GCF_004005485.1_ASM400548v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:35,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:35,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:35,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83743938-5c56-4543-bc2a-1c5d977d2081/dqc_reference/checkm_data
[2024-01-24 14:31:35,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:35,474] [INFO] Task started: CheckM
[2024-01-24 14:31:35,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005485.1_ASM400548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005485.1_ASM400548v1_genomic.fna/checkm_input GCF_004005485.1_ASM400548v1_genomic.fna/checkm_result
[2024-01-24 14:32:08,317] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:08,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:08,333] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:08,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:08,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005485.1_ASM400548v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:08,333] [INFO] Task started: Blastn
[2024-01-24 14:32:08,333] [INFO] Running command: blastn -query GCF_004005485.1_ASM400548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83743938-5c56-4543-bc2a-1c5d977d2081/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005485.1_ASM400548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:09,912] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:09,915] [INFO] Selected 24 target genomes.
[2024-01-24 14:32:09,915] [INFO] Target genome list was writen to GCF_004005485.1_ASM400548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:09,927] [INFO] Task started: fastANI
[2024-01-24 14:32:09,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg0966c40a-7a0d-49e4-a6d0-907ac15d94e5/GCF_004005485.1_ASM400548v1_genomic.fna.gz --refList GCF_004005485.1_ASM400548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005485.1_ASM400548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:29,066] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:29,080] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:29,081] [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_004005485.1	s__Sphingobium algorifonticola	100.0	1257	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002953135.1	s__Sphingobium sp002953135	80.1465	527	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196635.1	s__Sphingobium fontiphilum	79.9547	470	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967075.1	s__Sphingobium amiense	79.692	501	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007830065.1	s__Sphingobium wenxiniae	79.5721	436	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.17	98.76	0.86	0.79	4	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	79.5688	471	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
GCF_001556865.1	s__Sphingobium sp001556865	79.5431	457	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100475.1	s__Sphingobium faniae	79.4963	488	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	79.4412	458	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196495.1	s__Sphingobium jiangsuense	79.3941	477	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	79.3091	456	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650725.1	s__Sphingobium sp001650725	79.2519	501	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_014197035.1	s__Sphingobium scionense	79.2196	501	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911745.1	s__Sphingobium sp013911745	79.2044	376	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445065.1	s__Sphingobium quisquiliarum	79.1893	409	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_000447205.1	s__Sphingobium ummariense	79.027	479	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456115.1	s__Sphingobium baderi_A	79.0187	430	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248935.1	s__Sphingobium sp003248935	78.8834	454	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248505.1	s__Sphingobium sp003248505	78.5069	405	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012650175.1	s__Sphingomonas sp012650175	77.8061	295	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603885.1	s__Sphingobium sp018603885	77.7813	349	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449795.1	s__Sphingomonas sp018449795	77.6995	318	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114095.1	s__Sphingomonas sp900114095	77.5689	297	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871605.1	s__Sphingomonas_N sp903871605	77.1147	293	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:29,081] [INFO] GTDB search result was written to GCF_004005485.1_ASM400548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:29,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:29,085] [INFO] DFAST_QC result json was written to GCF_004005485.1_ASM400548v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:29,086] [INFO] DFAST_QC completed!
[2024-01-24 14:32:29,086] [INFO] Total running time: 0h1m29s